[Collab-qa-commits] r2547 - in packages-metadata: a b c d g h k l n o p r v
Charles Plessy
plessy at alioth.debian.org
Tue Nov 6 04:01:26 UTC 2012
Author: plessy
Date: 2012-11-06 04:01:25 +0000 (Tue, 06 Nov 2012)
New Revision: 2547
Added:
packages-metadata/a/ardesia.control
packages-metadata/a/ardesia.copyright
packages-metadata/b/beast.control
packages-metadata/b/beast.copyright
packages-metadata/b/biojava3-live.control
packages-metadata/b/biojava3-live.copyright
packages-metadata/c/camitk.control
packages-metadata/c/camitk.copyright
packages-metadata/d/dssp.control
packages-metadata/h/hmmer2.control
packages-metadata/h/hmmer2.copyright
packages-metadata/h/hmmer2.upstream
packages-metadata/k/king.control
packages-metadata/k/king.copyright
packages-metadata/k/knemo.control
packages-metadata/k/knemo.copyright
packages-metadata/k/komparator.control
packages-metadata/k/komparator.copyright
packages-metadata/l/libai-fann-perl.control
packages-metadata/l/libai-fann-perl.copyright
packages-metadata/l/libnhgri-blastall-perl.control
packages-metadata/l/libnhgri-blastall-perl.copyright
packages-metadata/l/librcsb-core-wrapper.control
packages-metadata/l/librcsb-core-wrapper.copyright
packages-metadata/l/libsort-key-top-perl.control
packages-metadata/l/libsort-key-top-perl.copyright
packages-metadata/n/ncbi-seg.control
packages-metadata/n/ncbi-seg.copyright
packages-metadata/n/ncbi-seg.upstream
packages-metadata/n/norsnet.control
packages-metadata/n/norsnet.copyright
packages-metadata/n/norsnet.upstream
packages-metadata/n/norsp.control
packages-metadata/n/norsp.copyright
packages-metadata/n/norsp.upstream
packages-metadata/o/oldsys-preseed.control
packages-metadata/o/oldsys-preseed.copyright
packages-metadata/p/predictnls.control
packages-metadata/p/predictnls.copyright
packages-metadata/p/predictnls.upstream
packages-metadata/p/profbval.control
packages-metadata/p/profbval.copyright
packages-metadata/p/profbval.upstream
packages-metadata/p/profisis.control
packages-metadata/p/profisis.copyright
packages-metadata/p/profisis.upstream
packages-metadata/p/python-biom-format.control
packages-metadata/p/python-biom-format.copyright
packages-metadata/p/python-biom-format.upstream
packages-metadata/r/r-bioc-biocgenerics.control
packages-metadata/r/r-bioc-biocgenerics.copyright
packages-metadata/r/r-cran-genabel.control
packages-metadata/v/vobcopy.control
packages-metadata/v/vobcopy.copyright
Modified:
packages-metadata/b/bowtie2.control
packages-metadata/d/debian-med.control
packages-metadata/g/genometools.control
packages-metadata/k/kradio4.control
packages-metadata/p/python-markdown.control
packages-metadata/r/r-bioc-qvalue.copyright
Log:
Daily automatic umegaya push
Added: packages-metadata/a/ardesia.control
===================================================================
--- packages-metadata/a/ardesia.control (rev 0)
+++ packages-metadata/a/ardesia.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,42 @@
+Source: ardesia
+Section: graphics
+Priority: extra
+Maintainer: TANIGUCHI Takaki <takaki at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev,
+ intltool,
+ pkg-config,
+ libgtk-3-dev,
+ libgsl0-dev,
+ libxml2-dev,
+ libgsf-1-dev
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/ardesia/
+Vcs-Git: git://git.debian.org/collab-maint/ardesia.git
+Vcs-Browser: http://git.debian.org/?p=collab-maint/ardesia.git;a=summary
+
+Package: ardesia
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ vlc,
+ xdg-utils
+Description: free digital sketchpad software
+ You can make colored free-hand annotations with digital ink everywhere,
+ record it and share on the network.
+ .
+ Thanks to Ardesia you are free to open any application
+ and fix your ideas and comments as if you wrote on a classic chalkboard.
+ You can use the tool to make effective on-screen presentation,
+ highlight things or point out things of interest.
+ The tool facilitates the online presentations and demos showing in real time
+ your computer screen to anyone in the network.
+ You can use this tool to enhance your lessons or courses working with
+ your preferred applications and your preferred operating system.
+ Create nice tutorial and demos saving the desktop images
+ with your free hand annotations.
+ Ardesia includes a sketchpad software that allow to free-hand draw
+ geometrical shapes using the shape recognizer.
+ .
+ Ardesia works with all the pointing device; you can use a mouse,
+ a touch screen, a drawing tablet, a cheap&professional wiimote whiteboard
+ or a commercial whiteboard, interactive projector and
+ any other devices supported by your operating system.
Added: packages-metadata/a/ardesia.copyright
===================================================================
--- packages-metadata/a/ardesia.copyright (rev 0)
+++ packages-metadata/a/ardesia.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ardesia
+Source: http://code.google.com/p/ardesia/
+
+Files: *
+Copyright: 2009-2010, Pilolli Pietro <pilolli.pietro at gmail.com>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2011 TANIGUCHI Takaki <takaki at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
Added: packages-metadata/b/beast.control
===================================================================
--- packages-metadata/b/beast.control (rev 0)
+++ packages-metadata/b/beast.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,114 @@
+Source: beast
+Section: gnome
+Priority: extra
+Maintainer: Debian Multimedia Maintainers <pkg-multimedia-maintainers at lists.alioth.debian.org>
+Uploaders:
+ Sam Hocevar (Debian packages) <sam+deb at zoy.org>,
+ Alessio Treglia <alessio at debian.org>
+Build-Depends:
+ autotools-dev,
+ debhelper (>= 7.0.50~),
+ gettext,
+ guile-1.8-dev (>= 1.6.4-2.1),
+ imagemagick,
+ libart-2.0-dev,
+ libasound2-dev,
+ libaudiofile-dev,
+ libcloog-ppl-dev,
+ libglib2.0-dev (>= 2.2.2),
+ libgnomecanvas2-dev,
+ libgtk2.0-dev (>= 2.2.2-2),
+ libmad0-dev,
+ libvorbis-dev,
+ libxml-parser-perl,
+ libxml2-utils
+Standards-Version: 3.9.2
+Vcs-Git: git://git.debian.org/pkg-multimedia/beast.git
+Vcs-Browser: http://git.debian.org/?p=pkg-multimedia/beast.git
+Homepage: http://beast.testbit.eu/
+
+Package: beast
+Architecture: any
+Depends:
+ libbse-0.7-4 (= ${binary:Version}),
+ ${misc:Depends},
+ ${shlibs:Depends}
+Recommends:
+ bse-alsa
+Breaks:
+ bse-alsa (<< 0.7.4)
+Suggests:
+ beast-doc
+Description: music synthesis and composition framework
+ BEAST/BSE is a plugin-based graphical system where you can link objects
+ to each other and generate sound.
+ .
+ BEAST also has support for scriptability in Scheme using Guile.
+
+Package: bse-alsa
+Section: sound
+Architecture: any
+Depends:
+ libbse-0.7-4 (= ${binary:Version}),
+ ${misc:Depends},
+ ${shlibs:Depends}
+Enhances:
+ beast
+Description: ALSA plugin for BEAST
+ BEAST/BSE is a plugin-based graphical system where you can link
+ objects to each other and generate sound.
+ .
+ This package provides a plugin for BEAST that uses ALSA (the
+ Advanced Linux Sound Architecture) to output sound.
+
+Package: libbse-0.7-4
+Section: libs
+Architecture: any
+Depends:
+ ${misc:Depends},
+ ${shlibs:Depends}
+Breaks:
+ beast (<< 0.7.4)
+Replaces:
+ beast (<< 0.7.4)
+Description: music synthesis and composition framework - shared library
+ BEAST/BSE is a plugin-based graphical system where you can link objects
+ to each other and generate sound.
+ .
+ This package provides the shared library.
+
+Package: libbse-dev
+Section: libdevel
+Architecture: all
+Depends:
+ libbse-0.7-4 (<< ${source:Upstream-Version}+1~),
+ libbse-0.7-4 (>= ${source:Version}),
+ libglib2.0-dev,
+ libgtk2.0-dev,
+ ${misc:Depends}
+Breaks:
+ beast (<< 0.7.4)
+Replaces:
+ beast (<< 0.7.4)
+Suggests:
+ beast-doc
+Description: music synthesis and composition framework - development files
+ BEAST/BSE is a plugin-based graphical system where you can link objects
+ to each other and generate sound.
+ .
+ This package provides the development files.
+
+Package: beast-doc
+Section: doc
+Architecture: all
+Depends:
+ ${misc:Depends}
+Breaks:
+ beast (<< 0.7.4)
+Replaces:
+ beast (<< 0.7.4)
+Description: Documentation for BEAST/BSE
+ BEAST/BSE is a plugin-based graphical system where you can link objects
+ to each other and generate sound.
+ .
+ This package provides the documentation files.
Added: packages-metadata/b/beast.copyright
===================================================================
--- packages-metadata/b/beast.copyright (rev 0)
+++ packages-metadata/b/beast.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,124 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Beast
+Upstream-Contact:
+ Tim Janik <timj at gtk.org>
+ Stefan Westerfeld <stefan at twc.de>
+ Olaf Hoehmann <olaf at gtk.org>
+Source: http://dist.testbit.eu/beast/v0.7/
+
+Files: *
+Copyright:
+ 2000-2008 Stefan Westerfeld <stefan at space.twc.de>
+ 1996-2008 Tim Janik <timj at gtk.org>
+ 2000-2002 Richard W.E. Furse, Paul Barton-Davis
+ 1998 Andy Sloane
+ 1999, 2000 David A. Bartold
+ 2004 Artem Popov <tfwo at mail.ru>
+ 2001 Matthias Kretz <kretz at kde.org>
+ 1998-2002 Tim Janik and Red Hat, Inc
+ 1997-2000 the GTK+ Team and others
+ 1995-1997 Peter Mattis, Spencer Kimball and Josh MacDonald
+ 2000 Michael Natterer <mitch at gimp.org>
+License: LGPL-2.1+
+
+Files: sfi/toyprof.{c,h} sfi/toyprof-mem.{c,h} sfi/gbsearcharray.h
+ bse/bsefilter-ellf.c bse/bsefilter.cc bse/bsefilter.h
+Copyright:
+ 2000-2006 Tim Janik
+ 1984, 1987, 1988, 1989, 1995, 2000 Stephen L. Moshier
+License: other-1
+
+Files: launchers/*
+Copyright: No copyright holders
+License: other-1
+
+Files: sfi/toyprof.pl
+Copyright: 2001 Tim Janik
+License: other-2
+
+Files: mkrelease.sh
+Copyright: 2010 Tim Janik
+License: other-3
+
+Files: ./plugins/freeverb/allpass.*
+ plugins/freeverb/comb.cpp
+ plugins/freeverb/tuning.h
+ plugins/freeverb/revmodel.*
+Copyright: no copyright holders
+License: public-domain
+ Written by Jezar at Dreampoint, June 2000
+ http://www.dreampoint.co.uk
+ This code is public domain
+
+Files: plugins/freeverb/denormals.h
+Copyright: no copyright holders
+License: public-domain
+ Macro for killing denormalled numbers
+ .
+ Written by Jezar at Dreampoint, June 2000
+ http://www.dreampoint.co.uk
+ Based on IS_DENORMAL macro by Jon Watte
+ This code is public domain
+
+Files: debian/*
+Copyright:
+ 2011 Alessio Treglia <alessio at debian.org>
+ 2003-2008 Sam Hocevar (Debian packages) <sam+deb at zoy.org>
+ 2001-2002 Junichi Uekawa <dancer at debian.org>
+License: LGPL-2.1+
+
+License: LGPL-2.1+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+Comment: You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU Lesser General Public
+ License can be found in `/usr/share/common-licenses/LGPL-2.1'
+
+License: other-1
+ This software is provided "as is"; redistribution and modification
+ is permitted, provided that the following disclaimer is retained.
+ .
+ This software is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ In no event shall the authors or contributors be liable for any
+ direct, indirect, incidental, special, exemplary, or consequential
+ damages (including, but not limited to, procurement of substitute
+ goods or services; loss of use, data, or profits; or business
+ interruption) however caused and on any theory of liability, whether
+ in contract, strict liability, or tort (including negligence or
+ otherwise) arising in any way out of the use of this software, even
+ if advised of the possibility of such damage.
+
+License: other-2
+ This code is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+License: other-3
+ This work is provided "as is"; redistribution and modification
+ in whole or in part, in any medium, physical or electronic is
+ permitted without restriction.
+ .
+ This work is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ .
+ In no event shall the authors or contributors be liable for any
+ direct, indirect, incidental, special, exemplary, or consequential
+ damages (including, but not limited to, procurement of substitute
+ goods or services; loss of use, data, or profits; or business
+ interruption) however caused and on any theory of liability, whether
+ in contract, strict liability, or tort (including negligence or
+ otherwise) arising in any way out of the use of this software, even
+ if advised of the possibility of such damage.
Added: packages-metadata/b/biojava3-live.control
===================================================================
--- packages-metadata/b/biojava3-live.control (rev 0)
+++ packages-metadata/b/biojava3-live.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,72 @@
+Source: biojava3-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-cli-java, libguava-java (>= 11.0.1),
+ default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), libjgrapht-java,
+ ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava3.0-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections-java (>= 2.1),
+ libcommons-dbcp-java (>= 1.1),
+ libhsqldb-java,
+ libbytecode-java,
+ jmol-applet, icedtea-netx,
+ libjson-simple-java
+Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
+Description: Java API to biological data and applications (version 3)
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
+ .
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+
+Package: libbiojava3-java
+Architecture: all
+Depends: libbiojava3.0-java, ${misc:Depends}
+Provides: libbiojava3-java
+Description: Java API to biological data and applications (default version)
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ This is a wrapper package which should enable smooth upgrades to new
+ versions.
+
+Package: libbiojava3-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+Suggests: libbiojava3-java-demos, libbiojava3-java
+Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.
+
Added: packages-metadata/b/biojava3-live.copyright
===================================================================
--- packages-metadata/b/biojava3-live.copyright (rev 0)
+++ packages-metadata/b/biojava3-live.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,73 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biojava3
+Source: http://www.biojava.org/
+
+Files: biojava3-forester
+Copyright: 2008-2009 Christian M. Zmasek
+ 2008-2009 Burnham Institute for Medical Research
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: *
+Copyright: 2008-2012 the Individual authors who contributed the code,
+ as identified by the @authors tag of the respective source file.
+ BioJava Developers <biojava-l at biojava.org>
+ Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
+ Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
+ Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
+ Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
+ A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
+ Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
+ Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Modified: packages-metadata/b/bowtie2.control
===================================================================
--- packages-metadata/b/bowtie2.control 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/b/bowtie2.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -8,6 +8,7 @@
Carlos Borroto <carlos.borroto at gmail.com>
Build-Depends: debhelper (>= 9.0), help2man
Standards-Version: 3.9.3
+XS-Testsuite: autopkgtest
Homepage: http://bowtie-bio.sourceforge.net/bowtie2
Vcs-Browser: http://git.debian.org/?p=debian-med/bowtie2.git
Vcs-Git: git://git.debian.org/debian-med/bowtie2.git
Added: packages-metadata/c/camitk.control
===================================================================
--- packages-metadata/c/camitk.control (rev 0)
+++ packages-metadata/c/camitk.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,67 @@
+Source: camitk
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>, Mathieu Malaterre <malat at debian.org>, Emmanuel Promayon <Emmanuel.Promayon at imag.fr>
+Build-Depends: debhelper (>= 9), cmake (>= 2.6), libvtk5-dev (>= 5.6), libqt4-dev (>= 4.6), libvtk5-qt4-dev (>= 5.6), xsdcxx (>= 3.2), libinsighttoolkit3-dev (>= 3.18), libxerces-c-dev (>= 3.1), libxml2-dev (>= 2.7), libgdcm2-dev (>= 2.0), libfftw3-dev, libqtwebkit-dev | libqt4-dev (<< 4.7)
+Build-Depends-Indep: doxygen, graphviz
+Standards-Version: 3.9.3
+Homepage: http://camitk.imag.fr/
+X-Homepage: https://forge.imag.fr/projects/camitk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/camitk/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/camitk/trunk/
+
+Package: libcamitk3
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Computer Assisted Medical Intervention Tool Kit - runtime
+ Helps researchers and clinicians to easily and rapidly collaborate in
+ order to prototype CAMI applications, that feature medical images,
+ surgical navigation and biomechanical simulations.
+ .
+ This package contains the shared libraries needed to run CamiTK applications.
+
+Package: libcamitk3-dev
+Architecture: any
+Section: libdevel
+Depends: libcamitk3 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends}
+Description: Computer Assisted Medical Intervention Tool Kit - development
+ Helps researchers and clinicians to easily and rapidly collaborate in
+ order to prototype CAMI applications, that feature medical images,
+ surgical navigation and biomechanical simulations.
+ .
+ This package contains development files needed to build CamiTK applications.
+ This package also provides the CamiTK wizard to create new extensions.
+
+Package: libcamitk3-data
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Description: Computer Assisted Medical Intervention Tool Kit - data
+ Helps researchers and clinicians to easily and rapidly collaborate in
+ order to prototype CAMI applications, that feature medical images,
+ surgical navigation and biomechanical simulations.
+ .
+ This package contains the example and test data for CamiTK.
+
+Package: libcamitk3-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Description: Computer Assisted Medical Intervention Tool Kit - documentation
+ Helps researchers and clinicians to easily and rapidly collaborate in
+ order to prototype CAMI applications, that feature medical images,
+ surgical navigation and biomechanical simulations.
+ .
+ This package contains the documentation for CamiTK.
+
+Package: camitk-imp
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: flagship application for the CamiTK library
+ CamiTK Helps researchers and clinicians to easily and rapidly collaborate in
+ order to prototype CAMI applications, that feature medical images,
+ surgical navigation and biomechanical simulations.
+ .
+ imp is the CamiTK flagship application.
Added: packages-metadata/c/camitk.copyright
===================================================================
--- packages-metadata/c/camitk.copyright (rev 0)
+++ packages-metadata/c/camitk.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,144 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: CamiTK
+Upstream-Contact: Emmanuel Promayon <Emmanuel.Promayon at imag.fr>,
+ Celine Fouard <Celine.Fouard at imag.fr>
+Source: https://forge.imag.fr/frs/?group_id=184
+
+Files: *
+Copyright: © 2001-2012 Emmanuel Promayon <Emmanuel.Promayon at imag.fr>, Celine Fouard <Celine.Fouard at imag.fr>
+ © 2001-2012 UJF-Grenoble 1, CNRS, TIMC-IMAG UMR 5525 (équipe GMCAO)
+License: LGPL-3+
+Comment: see also http://camitk.imag.fr/contributors.xml for a list of contributors
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+
+Files: tools/qtpropertybrowser/*
+Copyright: © 2010 Nokia Corporation and/or its subsidiary(-ies).
+ © 2001-2012 Emmanuel Promayon <Emmanuel.Promayon at imag.fr> for adding support of QVector3
+License: BSD
+Comment: see original sources at http://qt.gitorious.org/qt-solutions/qt-solutions/trees/master/qtpropertybrowser
+
+Files: actions/mesh/meshprocessing/tetgen1.4.3/*
+Copyright: © Copyright 2002, 2004, 2005, 2006
+ Hang Si
+ Rathausstr. 9, 10178 Berlin, Germany
+ si at wias-berlin.de
+License: MIT
+Comment: downloaded from http://tetgen.org/files/tetgen1.4.3.tar.gz, no modifications (two files are not distributed here: example.poly and makefile)
+
+Files: tools/mml/schema/generated/*
+Copyright: © 2005-2008 Code Synthesis Tools CC
+License: GPL-2+exception
+Comment: This directory contains files automatically generated by CodeSynthesis XSD from an XML Schema (C++ data binding compiler).
+
+Files: tools/mml/monitoring/tools/Xmlhighlighter.*
+Copyright: © Copyright 2009-10 Martin Holmes, Meagan Timney and the University of Victoria Humanities Computing and Media Centre.
+License: LGPL-2.1
+ see `/usr/share/common-licenses/LGPL-2.1'
+Comment: This file is part of the projXMLEditor project which in turn belongs to the Image Markup Tool version 2.0
+
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.
+ 3. Neither the name of Nokia Corporation and its Subsidiary(-ies) nor
+ the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: GPL-2+exception
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License version 2 as
+ published by the Free Software Foundation.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ In addition, as a special exception, Code Synthesis Tools CC gives
+ permission to link this program with the Xerces-C++ library (or with
+ modified versions of Xerces-C++ that use the same license as Xerces-C++),
+ and distribute linked combinations including the two. You must obey
+ the GNU General Public License version 2 in all respects for all of
+ the code used other than Xerces-C++. If you modify this copy of the
+ program, you may extend this exception to your version of the program,
+ but you are not obligated to do so. If you do not wish to do so, delete
+ this exception statement from your version.
+ .
+ Furthermore, Code Synthesis Tools CC makes a special exception for
+ the Free/Libre and Open Source Software (FLOSS) which is described
+ in the accompanying FLOSSE file.
+
+License: LGPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
+ in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
+ version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ Distribution of modified versions of this code is permissible UNDER
+ THE CONDITION THAT THIS CODE AND ANY MODIFICATIONS MADE TO IT IN THE
+ SAME SOURCE FILES tetgen.h AND tetgen.cxx REMAIN UNDER COPYRIGHT OF
+ THE ORIGINAL AUTHOR, BOTH SOURCE AND OBJECT CODE ARE MADE FREELY
+ AVAILABLE WITHOUT CHARGE, AND CLEAR NOTICE IS GIVEN OF THE
+ MODIFICATIONS.
+ .
+ Distribution of this code for any commercial purpose is permissible
+ ONLY BY DIRECT ARRANGEMENT WITH THE COPYRIGHT OWNER.
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
Modified: packages-metadata/d/debian-med.control
===================================================================
--- packages-metadata/d/debian-med.control 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/d/debian-med.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -26,42 +26,39 @@
Replaces: med-common
Provides: med-common
Description: Debian Med general config package
- This package provides the basic infrastructure of all med-* packages and is
- needed by them.
+ This package provides the basic infrastructure of all metapackages assembled
+ by the Debian Med team.
.
- This package provides some files which are common to all med-* packages.
- Moreover it introduces a method to handle system users in a group
- med using debconf.
+ This metapackage provides common features shared between the different
+ metapackages of the project. Moreover it introduces a method to handle a
+ 'med' system users group using debconf.
.
- Other packages in Debian Med Project are:
+ The Debian Med Project include metapackages for different tasks, which are:
+ * applications for microbiological research and support for development of
+ biological applications
+ * cloud computing in microbiological research
+ * drug databases
+ * dental surgery practice
+ * epidemiology and medical statistics
+ * image processing and support for imaging application development
+ * pharmacological research
+ * radiation oncology, diagnostic imaging and related fields
+ * medical practice
+ * psychological research and practice
+ * rehabilitation
+ * typesetting and publishing
+ * miscellaneous tools
.
- * med-bio biological research
- * med-bio-dev developing applications in biological research
- * med-cloud command line biol. applications for cloud computing
- * med-data drug databases
- * med-dental helping tools for dentists
- * med-epi epidemiology
- * med-imaging image processing
- * med-imaging-dev developing applications for image processing
- * med-pharmacy pharmaceutical research
- * med-physics radiation oncology, diagnostic imaging, related fields
- * med-practice general practitioners
- * med-psychology psychological research
- * med-statistics miscellaneous tools medical for statistics
- * med-tools contains miscellaneous tools
- * med-typesetting depends from useful tools for typesetting
- .
- Note: All these packages are so called metapackages. This means they are not
- executable programs, but only links to other packages. This way you will
- conveniently get all the non-commercial medical software which is available
- for Debian GNU/Linux.
+ Each task is represented by a metapackage. Metapackages do not contain
+ executable programs, but rather dependencies from other packages. This way
+ you will conveniently get all free medical software which is available for
+ Debian by simply installing the relevant metapackage
-
Package: med-bio
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gassst, gbrowse, gdpc, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
-Suggests: abyss, act, agdbnet, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, beads, beast-mcmc, big-blast, bio-mauve, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, chado, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, eigensoft, elph, embassy-phylip, emboss-explorer, emboss-kaptain, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fasttree, figaro, finex, fluctuate, forester, forge, galaxy, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, igv, jbrowse, jigsaw, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, molphy, mozilla-biofox, msatfinder, mugsy, mummergpu, murasaki, mview, neobio, ngila, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phylowin, plato, prank, proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, sequenceconverter.app, sift, smalt, snap, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tophat, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve, trf, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zodiac
+Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
+Suggests: abyss, act, agdbnet, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, beads, beast-mcmc, big-blast, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, sequenceconverter.app, sift, smalt, snap, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden
Description: Debian Med micro-biology packages
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
@@ -69,8 +66,8 @@
Package: med-bio-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libpal-java, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
-Suggests: bioclipse, biostrings, iranges, libajax6-dev, libbio-das-perl, libgbfp-dev, libgff-perl, libmems-1.5-1, libnucleus6-dev, libqsearch-dev, librg-blast-parser-perl, libsbml5-dev, octave-bioinfo, pysam, python-mmtk, r-cran-rocr
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libai-fann-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libbiojava3-java, libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, libhmsbeagle-dev, libjebl2-java, libncbi6-dev, libpal-java, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsort-key-top-perl, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
+Suggests: bioclipse, biostrings, iranges, libbio-das-perl, libforester-java, libgbfp-dev, libgenometools0-dev, libgff-perl, libmems-1.5-1, libnhgri-blastall-perl, libopenmm4-dev, libqsearch-dev, librcsb-core-wrapper0-dev, libsbml5-dev, octace-bioinfo, octave-bioinfo, pysam, python-biom-format, python-librcsb-core-wrapper, python-mmtk, r-bioc-biocgenerics, r-cran-rocr
Description: Debian Med packages for development of micro-biology applications
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
@@ -89,18 +86,18 @@
Package: med-data
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: python-hl7
-Suggests: drugref.org, freediams
+Recommends: freediams, freemedforms-freedata, python-hl7
+Suggests: drugref.org
Description: Debian Med drug databases
- There is at least one free medical drug database packaged for Debian
- which can be installed using this metapackage. It is supported by the
- GNUmed Electronic Medical Record package.
+ This metapackage will install free drug databases and related
+ applications. The database can be accessed by any EMR using
+ the application.
Package: med-dental
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: imagetooth
-Suggests: openmolar
+Suggests: entangle, openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
@@ -120,8 +117,8 @@
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap, amide, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
-Suggests: afni, ants, bioimagesuite, bioimagexd, blox, brainvisa, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, dcm4che, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, insightapplications, invesalius, isis, jemris, jist, kradview, libvista2, lipsia, maris, mayam, medisnap, mesa-test-tools, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
+Recommends: aeskulap, amide, ants, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, king, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
+Suggests: afni, bioimagesuite, bioimagexd, blox, brainvisa, camitk-imp, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, crea, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, incf-nidash-oneclick-clients, insightapplications, invesalius, isis, jemris, jist, kradview, libdcm4che-java, libvista2, lipsia, maris, mayam, medisnap, mesa-test-tools, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, orthanc, paraview, piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -144,8 +141,8 @@
Package: med-imaging-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: cimg-dev, ctn-dev, gmic, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libopenslide-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat
-Suggests: emokit, igstk-examples, insighttoolkit3-examples, libactiviz.net5.6-cil, libbio-formats-java, libctkcore0-dev, libeegdev-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libvista2-dev, libvtk5.4, libxdffileio-dev, python-libavg, python-openslide
+Recommends: cimg-dev, ctn-dev, gmic, libactiviz.net-cil, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libopenslide-dev, libvia-dev, libvolpack1-dev, libvtk5-dev, libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat
+Suggests: emokit, igstk-examples, insighttoolkit3-examples, libbio-formats-java, libcamitk3-dev, libctkcore0-dev, libeegdev-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libteem1-dev, libvista2-dev, libvtk5.4, libxdffileio-dev, octave-dicom, python-libavg, python-openslide
Description: Debian Med packages for medical image development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing.
@@ -159,7 +156,7 @@
This metapackage will install tools that are useful for radiation
oncology.
-Package: med-pharmacy
+Package: med-pharma
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: chemtool
@@ -183,8 +180,8 @@
Package: med-practice
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: clinica, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
-Suggests: clearhealth, elementalclinic, elexis, freeb, freediams, freeicd, freemed, freemedforms, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
+Recommends: clinica, freediams, freemedforms-emr, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
+Suggests: clearhealth, elementalclinic, elexis, entangle, freeb, freeicd, freemed, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
@@ -201,8 +198,8 @@
Package: med-rehabilitation
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: sitplus
-Suggests: aghermann
+Recommends:
+Suggests: aghermann, sitplus
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
@@ -210,7 +207,7 @@
Package: med-statistics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: r-bioc-edger, r-bioc-limma, r-cran-pvclust, r-cran-qvalue, r-cran-randomforest
+Recommends: r-bioc-edger, r-bioc-limma, r-bioc-qvalue, r-cran-pvclust, r-cran-randomforest
Suggests: r-cran-beeswarm, science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
@@ -220,7 +217,7 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: edfbrowser, hunspell-de-med, pcalendar, pondus, quitcount, wgerman-medical, workrave
-Suggests: cl-pubmed, cycle, hunspell-en-med, mencal, mssstest, python-clips
+Suggests: cl-pubmed, cycle, entangle, hunspell-en-med, mencal, mssstest, python-clips
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
@@ -228,8 +225,8 @@
Package: med-typesetting
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: texlive-latex-extra, texlive-science
-Suggests: bibus, jabref-plugin-oo, kbibtex, referencer
+Recommends: king, texlive-latex-extra, texlive-science
+Suggests: biber, bibus, jabref-plugin-oo, kbibtex, referencer
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
Added: packages-metadata/d/dssp.control
===================================================================
--- packages-metadata/d/dssp.control (rev 0)
+++ packages-metadata/d/dssp.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,44 @@
+Source: dssp
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Maarten L. Hekkelman <m.hekkelman at cmbi.ru.nl>,
+ Laszlo Kajan <lkajan at rostlab.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.0.50~),
+ libboost-filesystem-dev (>= 1.42.0.1),
+ libboost-iostreams-dev (>= 1.42.0.1),
+ libboost-program-options-dev (>= 1.42.0.1),
+ libboost-system-dev (>= 1.42.0.1),
+ libboost-thread-dev (>= 1.42.0.1)
+Standards-Version: 3.9.3
+Section: science
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dssp/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dssp/trunk/
+DM-Upload-Allowed: yes
+Homepage: http://www.cmbi.ru.nl/dssp.html
+
+Package: dssp
+Architecture: any
+Depends: ${misc:Depends}, ${shlibs:Depends}
+Description: protein secondary structure assignment based on 3D structure
+ DSSP is an application you use to assign the secondary structure of a protein
+ based on its solved three dimensional (3D) structure.
+ .
+ This version (2) of DSSP is a rewrite that produces the same output as the
+ original DSSP, but deals better with exceptions in PDB files and is much
+ faster.
+
+Package: dssp-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: dssp (= ${binary:Version}), ${misc:Depends}
+Description: debugging symbols for dssp
+ DSSP is an application to assign the secondary structure of a protein
+ based on its three dimensional (3D) structure.
+ .
+ This version (2) of DSSP is a rewrite that produces the same output as the
+ original DSSP, but deals better with exceptions in PDB files and is much
+ faster.
+ .
+ This package provides the detached debug symbols for dssp.
Modified: packages-metadata/g/genometools.control
===================================================================
--- packages-metadata/g/genometools.control 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/g/genometools.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -5,7 +5,9 @@
Build-Depends: debhelper (>= 9),
liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev,
liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev,
- libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev
+ libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev,
+ texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor,
+ texlive-fonts-recommended
Standards-Version: 3.9.4
DM-Upload-Allowed: yes
Homepage: http://genometools.org
@@ -40,8 +42,7 @@
Description: versatile genome analysis library
This package contains the GenomeTools shared library and header
files. It offers efficient sequence analysis components, available
- via an object-oriented interface, and a collection of useful tools for
- bioinformatics, combined into a single binary.
+ via an object-oriented interface.
.
Besides basic bioinformatics data structures, the library contains components
for sequence and annotation handling, sequence compression, index structure
@@ -54,8 +55,13 @@
libgenometools0 (= ${binary:Version})
Section: libdevel
Description: development files for GenomeTools
- This package contains the GenomeTools static libraries and necessary
+ This package contains the GenomeTools static library and necessary
header files.
+ .
+ Besides basic bioinformatics data structures, the library contains components
+ for sequence and annotation handling, sequence compression, index structure
+ generation and access, efficient matching, annotation visualization and much
+ more.
Package: genometools-doc
Architecture: all
@@ -63,7 +69,9 @@
Section: doc
Description: documentation for GenomeTools
This package contains API documentation and tool documentation for
- GenomeTools.
+ GenomeTools. The GenomeTools toolkit contains binaries for sequence and
+ annotation handling, sequence compression, index structure generation and
+ access, annotation visualization, and much more.
Package: genometools-dbg
Architecture: any
Added: packages-metadata/h/hmmer2.control
===================================================================
--- packages-metadata/h/hmmer2.control (rev 0)
+++ packages-metadata/h/hmmer2.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,63 @@
+Source: hmmer2
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Matthew Vernon <matthew at debian.org>,
+ Nelson A. de Oliveira <naoliv at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8), pvm-dev, autotools-dev
+Standards-Version: 3.9.3
+Homepage: http://hmmer.janelia.org/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hmmer2/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hmmer2/trunk/
+
+Package: hmmer2
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: biosquid
+Suggests: hmmer2-doc (>= ${source:Version}), hmmer2-pvm (>= ${binary:Version})
+Description: profile hidden Markov models for protein sequence analysis
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+
+Package: hmmer2-pvm
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, pvm
+Suggests: hmmer2-doc (>= ${binary:Version})
+Description: HMMER programs with PVM (Parallel Virtual Machine) support
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ .
+ This package contains HMMER programs compiled with PVM support.
+
+Package: hmmer2-doc
+Section: doc
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: hmmer2 (>= ${source:Version}), xpdf-reader | pdf-viewer
+Description: profile hidden Markov models for protein sequence analysis (docs)
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ .
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ .
+ This package contains documents and example files for the hmmer2 package.
Added: packages-metadata/h/hmmer2.copyright
===================================================================
--- packages-metadata/h/hmmer2.copyright (rev 0)
+++ packages-metadata/h/hmmer2.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,34 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: hmmer
+Upstream-Contact: Sean Eddy <eddy at genetics.wustl.edu>
+Source: ftp://selab.janelia.org/pub/software/hmmer/
+
+Files: debian/*
+Copyright: 1998, John Lapeyre <lapeyre at physics.arizona.edu>
+License: GPL-2+
+
+Files: *
+Copyright: Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
Added: packages-metadata/h/hmmer2.upstream
===================================================================
--- packages-metadata/h/hmmer2.upstream (rev 0)
+++ packages-metadata/h/hmmer2.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,15 @@
+Contact: http://selab.janelia.org/people/eddys/contact.html
+DOI: 10.1093/bioinformatics/14.9.755
+Name: HMMER
+Homepage: http://hmmer.janelia.org
+PMID: 9918945
+Reference:
+ Author: Eddy, SR
+ Title: Profile hidden Markov models
+ Journal: Bioinformatics
+ Volume: 14
+ Number: 9
+ Pages: 755-763
+ Year: 1998
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Added: packages-metadata/k/king.control
===================================================================
--- packages-metadata/k/king.control (rev 0)
+++ packages-metadata/k/king.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,48 @@
+Source: king
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 9), default-jdk, javahelper, ant, libitext-java,
+ libjogl-java
+Standards-Version: 3.9.3
+Homepage: http://kinemage.biochem.duke.edu/software/king.php
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/king/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/king/
+
+Package: king
+Architecture: all
+Depends: ${misc:Depends}, ${java:Depends}
+Description: interactive system for three-dimensional vector graphics
+ KiNG (Kinemage, Next Generation) is an interactive system for
+ three-dimensional vector graphics. It supports a set of graphics
+ primitives that make it suitable for many types of graphs, plots, and
+ other illustrations; although its first use was to display
+ macromolecular structures for biophysical research. KiNG builds on Mage,
+ JavaMage, and the "kinemage" (kinetic image) concept to deliver a
+ full-featured Java application with a user-friendly interface and
+ integrated editing features. The KiNG jar file can be used within a web
+ page as a Java applet or Java object to promote easy access to kinemages
+ or coordinate files from a web browser.
+
+# --> see README.source
+#Package: king-java-doc
+#Architecture: all
+#Depends: ${misc:Depends}, ${java:Depends}
+#Description: interactive system for three-dimensional vector graphics (Java API docs)
+# KiNG (Kinemage, Next Generation) is an interactive system for
+# three-dimensional vector graphics. It supports a set of graphics
+# primitives that make it suitable for many types of graphs, plots, and
+# other illustrations; although its first use was to display
+# macromolecular structures for biophysical research. KiNG builds on Mage,
+# JavaMage, and the "kinemage" (kinetic image) concept to deliver a
+# full-featured Java application with a user-friendly interface and
+# integrated editing features. The KiNG jar file can be used within a web
+# page as a Java applet or Java object to promote easy access to kinemages
+# or coordinate files from a web browser.
+# .
+# This package provides the documentation of the Java API documentation
+# of KiNG and the components used by King. It is dedicated at programmers
+# who want to program Java code using classes from KiNG. The documentation
+# for plain usage of KiNG is part of the king package.
Added: packages-metadata/k/king.copyright
===================================================================
--- packages-metadata/k/king.copyright (rev 0)
+++ packages-metadata/k/king.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,56 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: KiNG
+Upstream-Contact: Vincent B. Chen <vincent.chen at duke.edu>
+Source: http://kinemage.biochem.duke.edu/software/king.php
+
+Files: *
+Copyright: 2002-2011 Ian W. Davis <ian.w.davis at gmail.com>,
+ Vincent B. Chen <vincent.chen at duke.edu>
+License: KiNG-License
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ 3. The end-user documentation included with the redistribution, if any, must
+ include the following acknowledgment:
+ .
+ "This product includes software developed in the Richardon lab at Duke
+ University (http://kinemage.biochem.duke.edu)."
+ .
+ Alternately, this acknowledgment may appear in the software itself, if and
+ wherever such third-party acknowledgments normally appear.
+ .
+ 4. The name of the copyright holder, the names of the contributors, and the
+ names "KiNG", "Kinemage, Next Generation", and "Mage" must not be used to
+ endorse or promote products derived from this software without prior
+ written permission.
+ 5. Products derived from this software may not be called "KiNG", nor may
+ "KiNG" appear in their name, without prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ .
+ This license is based on the BSD and Apache licenses.
+ See http://www.opensource.org/ for more details on these and other licenses.
+Comment: The Files driftwood-*-src/* are released under "The Driftwood License"
+ but this is just another name for the completely identical text as the "King
+ License" and copyright holders are identical as well.
+
+Files: debian/*
+Copyright: 2012 Andreas Tille <tille at debian.org>
+License: Apache-2.0
+ On Debian systems the complete text of the Apache-2.0 license can be found at
+ `/usr/share/common-licenses/Apache-2.0`.
+
Added: packages-metadata/k/knemo.control
===================================================================
--- packages-metadata/k/knemo.control (rev 0)
+++ packages-metadata/k/knemo.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,24 @@
+Source: knemo
+Section: kde
+Priority: optional
+Maintainer: Debian KDE Extras Team <pkg-kde-extras at lists.alioth.debian.org>
+Uploaders: Mark Purcell <msp at debian.org>, Felix Geyer <debfx-pkg at fobos.de>
+Build-Depends: debhelper (>= 9), pkg-kde-tools, cmake, kdelibs5-dev, kde-workspace-dev,
+ libiw-dev [linux-any],
+ libnl-3-dev [linux-any], libnl-route-3-dev [linux-any]
+Standards-Version: 3.9.2
+Homepage: http://extragear.kde.org/apps/knemo/
+Vcs-Svn: svn://svn.debian.org/pkg-kde/kde-extras/knemo/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/pkg-kde/kde-extras/knemo/trunk/
+
+
+Package: knemo
+Architecture: any
+Depends: systemsettings, libqt4-sql-sqlite, ${shlibs:Depends}, ${misc:Depends}
+Description: network interfaces monitor for KDE's systray
+ KNemo displays for every network interface an icon in the systray.
+ Tooltips and an info dialog provide further information about the
+ interface. Passive popups inform about interface changes.
+ A traffic plotter is also integrated.
+ .
+ knemo polls the network interface status every second.
Added: packages-metadata/k/knemo.copyright
===================================================================
--- packages-metadata/k/knemo.copyright (rev 0)
+++ packages-metadata/k/knemo.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,97 @@
+This package was debianized by Achim Bohnet <ach at mpe.mpg.de>
+on Mon, 28 Jun 2004 23:46:36 +0200
+
+It was downloaded from http://www.kde-apps.org/content/show.php?content=12956
+
+Upstream author is
+ Percy Leonhardt <percy at eris23.de>
+
+ Signal Plotter:
+ Taken from KSysGuard
+ Chris Schlaeger <cs at kde.org>
+
+Translation:
+ Zlatko Popov <zlatkopopov at fsa-bg.org> (bg)
+ Thierry Vignaud <tvignaud at mandriva.com> (br)
+ Jakub Friedl <jfriedl at suse.cz> Klara Cihlarova <koty at seznam.cz> (cs)
+ FULL NAME <EMAIL at ADDRESS> (cy)
+ Erik Kjær Pedersen <erik at binghamton.edu> (da)
+ Jannick Kuhr <jannick.kuhr at kdemail.net> (de)
+ Spiros Georgaras <sngeorgaras at otenet.gr> (el)
+ Malcolm Hunter <malcolm.hunter at gmx.co.uk> (en_GB)
+ Enrique Matias Sanchez (aka Quique) <cronopios at gmail.com> (es)
+ Marek Laane <bald at starman.ee> (et)
+ Julien Morot <julien at momonux.org> (fr)
+ Kevin Patrick Scannell <scannell at SLU.EDU> (ga)
+ Kroly Barcza (VectoR) <kbarcza at blackpanther.hu> (hu)
+ Samuele Kaplun <samuele.kaplun at collegiodimilano.it> (it)
+ Yukiko Bando <ybando at k6.dion.ne.jp> (ja)
+ Giasher <giasher at telenet.ge> (ka)
+ Donatas Glodenis <dgvirtual at akl.lt> (lt)
+ Bram Schoenmakers <bramschoenmakers at kde.nl> Rinse de Vries <rinsedevries at kde.nl> (nl)
+ Marcin Zasada <emzeta76 at gazeta.pl> (pl)
+ José Nuno Coelho Pires <jncp at netcabo.pt> (pt)
+ Lisiane Sztoltz Teixeira <lisiane at kdemail.net> (pt_BR)
+ Alexander Shiyan <shc at users.sourceforge.net> (ru)
+ Steve Murphy <murf at e-tools.com> (rw)
+ Slobodan Simic <simicsl at verat.net> (sr)
+ Slobodan Simic <simicsl at verat.net> (sr at Latn)
+ Stefan Asserhäll <stefan.asserhall at comhem.se> (sv)
+ Bulent SENER <bsener at inonu.edu.tr> (tr)
+
+Copyright:
+
+ Copyright (C) 2004-2006, Percy Leonhardt <percy at eris23.de>
+ Copyright (C) 2009-2010, John Stamp <jstamp at users.sourceforge.net>
+ Copyright (c) 1999-2002, Chris Schlaeger <cs at kde.org>
+ Copyright (c) 2006-2009, John Tapsell <tapsell at kde.org>
+ Copyright (c) 2007-2008, Thomas BERNARD <miniupnp at free.fr>
+ Copyright (c) 2002, Cornelius Schumacher <schumacher at kde.org>
+ Copyright (c) 2004, Tobias Koenig <tokoe at kde.org>
+ Copyright (c) 2003-2004, Reinhold Kainhofer <reinhold at kainhofer.com>
+ Copyright (c) 2002, David Jarvie <software at astrojar.org.uk>
+ Copyright (c) 2004, Bram Schoenmakers <bramschoenmakers at kde.nl>
+
+
+License:
+
+KNemo is licensed under the LGPL-2+:
+
+ KNemo is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Library General Public License as
+ published by the Free Software Foundation; either version 2 of
+ the License, or (at your option) any later version.
+
+ KNemo is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Library General Public License for more details.
+
+ You should have received a copy of the GNU Library General Public License
+ along with this library; see the file COPYING.LIB. If not, write to
+ the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+src/knemod/ksignalplotter_p.h and src/knemod/signalplotter.{cpp,.h} are licensed under the GPL-{2,3}:
+
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of version 2 of the GNU General Public
+ License as published by the Free Software Foundation.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+ KSysGuard is currently maintained by Chris Schlaeger <cs at kde.org>.
+ Please do not commit any changes without consulting me first. Thanks!
+
+
+ On Debian GNU/Linux systems, the complete text of the GNU Lesser General
+ Public License and the GNU General Public license can be found in
+ /usr/share/common-licenses/LGPL-2 file and /usr/share/common-licenses/GPL-2 file,
+ respectively.
Added: packages-metadata/k/komparator.control
===================================================================
--- packages-metadata/k/komparator.control (rev 0)
+++ packages-metadata/k/komparator.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,19 @@
+Source: komparator
+Section: kde
+Priority: optional
+Maintainer: Debian KDE Extras Team <pkg-kde-extras at lists.alioth.debian.org>
+Uploaders: Fathi Boudra <fabo at debian.org>, Mark Purcell <msp at debian.org>
+Build-Depends: debhelper (>= 9), cmake, gettext,
+ kdelibs5-dev (>= 4:4.4.4), pkg-kde-tools (>= 0.6.5)
+Standards-Version: 3.8.4
+Homepage: http://kde-apps.org/content/show.php?content=116039
+Vcs-Browser: http://svn.debian.org/wsvn/pkg-kde/kde-extras/komparator/trunk
+Vcs-Svn: svn://svn.debian.org/pkg-kde/kde-extras/komparator/trunk
+
+Package: komparator
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: directories comparator for KDE
+ Komparator is an application that searches and synchronizes two directories.
+ It discovers duplicate, newer or missing files and empty folders. It works on
+ local and network or kioslave protocol folders.
Added: packages-metadata/k/komparator.copyright
===================================================================
--- packages-metadata/k/komparator.copyright (rev 0)
+++ packages-metadata/k/komparator.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,121 @@
+This work was packaged for Debian by:
+
+ Fathi Boudra <fboudra at free.fr> on Tue, 1 Aug 2006 17:42:25 +0200.
+
+It was downloaded from:
+
+ http://kde-apps.org/content/show.php/komparator4?content=116039
+
+Upstream Author:
+
+ Georg Hennig <georg.hennig at web.de>
+
+Copyright:
+
+ Copyright (C) 2005-2010 Georg Hennig <georg.hennig at web.de>
+
+License:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+
+On Debian systems, the complete text of the GNU General
+Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+The Debian packaging is:
+
+ Copyright (C) 2006-2010 Fathi Boudra <fabo at debian.org>
+
+you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+Copyright for src/komparatorcomparejob.*:
+
+ Copyright (C) 2005-2010 Georg Hennig <georg.hennig at web.de>
+
+ This file uses main parts of "fdupes.c" from fdupes-1.40.
+ FDUPES Copyright (C) 1999 Adrian Lopez <adrian2 at caribe.net>
+
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation files
+ (the "Software"), to deal in the Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, sublicense, and/or sell copies of the Software,
+ and to permit persons to whom the Software is furnished to do so,
+ subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */
+
+Copyright for src/kmdcodec.*:
+
+ Copyright (C) 2000-2001 Dawit Alemayehu <adawit at kde.org>
+ Copyright (C) 2001 Rik Hemsley (rikkus) <rik at kde.org>
+
+ This program is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ RFC 1321 "MD5 Message-Digest Algorithm" Copyright (C) 1991-1992.
+ RSA Data Security, Inc. Created 1991. All rights reserved.
+
+ The KMD5 class is based on a C++ implementation of
+ "RSA Data Security, Inc. MD5 Message-Digest Algorithm" by
+ Mordechai T. Abzug, Copyright (c) 1995. This implementation
+ passes the test-suite as defined in RFC 1321.
+
+ The encoding and decoding utilities in KCodecs with the exception of
+ quoted-printable are based on the java implementation in HTTPClient
+ package by Ronald Tschal�r Copyright (C) 1996-1999.
+
+ The quoted-printable codec as described in RFC 2045, section 6.7. is by
+ Rik Hemsley (C) 2001.
+
+ KMD4 class based on the LGPL code of Copyright (C) 2001 Nikos Mavroyanopoulos
+ The algorithm is due to Ron Rivest. This code is based on code
+ written by Colin Plumb in 1993.
+
+Copyright for src/kdatecombo.*:
+
+ Copyright (C) 2008 Daniel Caleb Jones <danielcjones at gmail.com>
+
+The documentations provided with komparator is distributed under
+the GNU Free Documentation License (FDL). They are considered free with
+regards to the Debian Free Software Guidelines (DFSG) because they don't
+contain any unmodifiable parts (invariant sections).
+
+On Debian systems, the complete text of the GNU Free Documentation
+License can be found in `/usr/share/common-licenses/GFDL'.
+
+Komparator uses kquery.cpp, kquery.h, kdatecombo.cpp and kdatecombo.h taken
+without changes from kfind which is © Stephan Kulow <coolo at kde.org> and
+is licensed under the GPL, see above.
Modified: packages-metadata/k/kradio4.control
===================================================================
--- packages-metadata/k/kradio4.control 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/k/kradio4.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -5,7 +5,7 @@
Uploaders: Mark Purcell <msp at debian.org>
Build-Depends: debhelper (>= 9), pkg-kde-tools (>= 0.5), cmake,
kdelibs5-dev (>= 4:4.2.0), gettext, libsndfile1-dev, liblircclient-dev,
- libmms-dev, libvorbis-dev, libogg-dev, libavformat-dev, libglib2.0-dev,
+ libmms-dev, libvorbis-dev, libogg-dev, libavformat-dev, libglib2.0-dev, libboost-dev,
libmp3lame-dev, libasound2-dev [linux-any]
Standards-Version: 3.9.2
Homepage: http://kradio.sourceforge.net/
Added: packages-metadata/l/libai-fann-perl.control
===================================================================
--- packages-metadata/l/libai-fann-perl.control (rev 0)
+++ packages-metadata/l/libai-fann-perl.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,20 @@
+Source: libai-fann-perl
+Section: perl
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 7), libfann-dev (>= 2.1.0~beta~)
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/libai-fann-perl/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/libai-fann-perl/trunk/
+Homepage: http://leenissen.dk/fann/wp/
+
+Package: libai-fann-perl
+Section: perl
+Priority: optional
+Architecture: any
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}
+Description: Perl wrapper for the FANN library
+ This module provides a Perl wrapper for the FANN library
+ (http://leenissen.dk/fann/wp/).
Added: packages-metadata/l/libai-fann-perl.copyright
===================================================================
--- packages-metadata/l/libai-fann-perl.copyright (rev 0)
+++ packages-metadata/l/libai-fann-perl.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,24 @@
+This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
+Fri, 25 Nov 2011 18:25:46 +0100
+
+Upstream Authors:
+
+ Salvador Fandino <sfandino at yahoo.com>
+
+Copyright:
+
+ Copyright (C) 2006 by Salvador Fandino <sfandino at yahoo.com>
+
+License:
+
+ This Perl module is free software; you can redistribute it and/or
+ modify it under the same terms as Perl itself, either Perl version
+ 5.8.8 or, at your option, any later version of Perl 5 you may have
+ available.
+
+On Debian systems, the complete text of the Perl Artistic License can be
+found in `/usr/share/common-licenses/Artistic'.
+
+The Debian packaging is (C) 2011, Laszlo Kajan <lkajan at rostlab.org> and
+is licensed under the GPL. On Debian systems, the complete text of the GNU
+General Public License can be found in `/usr/share/common-licenses/GPL'.
Added: packages-metadata/l/libnhgri-blastall-perl.control
===================================================================
--- packages-metadata/l/libnhgri-blastall-perl.control (rev 0)
+++ packages-metadata/l/libnhgri-blastall-perl.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,22 @@
+Source: libnhgri-blastall-perl
+Section: perl
+Priority: optional
+Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>, Jens Preussner <jenzo at cbv.net>
+Build-Depends: debhelper (>= 8), perl
+Vcs-Git: git://git.debian.org/pkg-perl/packages/libnhgri-blastall-perl.git
+Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libnhgri-blastall-perl.git
+Standards-Version: 3.9.3
+Homepage: ftp://ftp.nhgri.nih.gov/pub/software/blastall/
+
+Package: libnhgri-blastall-perl
+Architecture: all
+Depends: ${perl:Depends}, ${misc:Depends}
+Description: Perl extension for running and parsing NCBI's BLAST 2.x
+ NHGRI::Blastall will enable usage of BLAST out of a Perl script, if BLAST2
+ or WU-BLAST are installed locally. Main features are:
+ * run BLAST (also via network, which requires blastcl3)
+ * BLAST single sequences against each other or against a given library
+ * format databases
+ * mask out repetitive DNA
+ * read, parse and filter existing BLAST reports
Added: packages-metadata/l/libnhgri-blastall-perl.copyright
===================================================================
--- packages-metadata/l/libnhgri-blastall-perl.copyright (rev 0)
+++ packages-metadata/l/libnhgri-blastall-perl.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,45 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Joseph Ryan <jfryan at nhgri.nih.gov>
+Source: ftp://ftp.nhgri.nih.gov/pub/software/blastall/NHGRI-Blastall-0.66.tar.gz
+
+Files: debian/*
+Copyright: 2009 Laszlo Kajan <lkajan at rostlab.org>
+ 2012 Jens Preußner <jenzo at cbv.net>
+License: Artistic or GPL-1+
+
+Files: *
+Copyright: public-domain
+License: public-domain
+ PUBLIC DOMAIN NOTICE
+ This software/database is ``United States Government Work'' under the
+ terms of the United States Copyright Act. It was written as part of
+ the authors' official duties for the United States Government and thus
+ cannot be copyrighted. This software/database is freely available to
+ the public for use without a copyright notice. Restrictions cannot
+ be placed on its present or future use.
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the National Human Genome
+ Research Institute (NHGRI) and the U.S. Government does not and cannot
+ warrant the performance or results that may be obtained by using this
+ software or data. NHGRI and the U.S. Government disclaims all
+ warranties as to performance, merchantability or fitness for any
+ particular purpose.
+ In any work or product derived from this material, proper attribution
+ of the authors as the source of the software or data should be made,
+ using http://genome.nhgri.nih.gov/webblast as the citation.
+
+License: Artistic
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic'.
+
+License: GPL-1+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 1, or (at your option)
+ any later version.
+ .
+ On Debian systems, the complete text of version 1 of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-1'.
Added: packages-metadata/l/librcsb-core-wrapper.control
===================================================================
--- packages-metadata/l/librcsb-core-wrapper.control (rev 0)
+++ packages-metadata/l/librcsb-core-wrapper.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,91 @@
+Source: librcsb-core-wrapper
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 7.3.5), doxygen, graphviz, libboost-python-dev, libxerces-c-dev,
+ python-all-dev (>= 2.6.6-3~), python-all-dbg,
+ libtool, bison, flex
+Standards-Version: 3.9.3
+Section: libs
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rcsb-core-wrapper/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rcsb-core-wrapper/trunk/
+DM-Upload-Allowed: yes
+Homepage: http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
+X-Python-Version: >= 2.5
+
+Package: librcsb-core-wrapper0
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: C++ library providing OO API to information in mmCIF format
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This package contains the shared library.
+
+Package: librcsb-core-wrapper0-dev
+Section: libdevel
+Architecture: any
+Depends: librcsb-core-wrapper0 (= ${binary:Version}), ${misc:Depends},
+Suggests: librcsb-core-wrapper0-dbg, librcsb-core-wrapper-doc
+Provides: librcsb-core-wrapper-dev
+Description: development files for librcsb-core-wrapper0
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This package contains files necessary for developing applications with
+ the library.
+
+Package: librcsb-core-wrapper-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: documentation for librcsb-core-wrapper0
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This package contains html documentation.
+
+Package: librcsb-core-wrapper0-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: librcsb-core-wrapper0 (= ${binary:Version}), ${misc:Depends}
+Enhances: librcsb-core-wrapper0-dev, python-corepywrap
+Description: debugging symbols for librcsb-core-wrapper0
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This package contains the detached debug symbols for the library and the
+ Python bindings.
+
+Package: python-corepywrap
+Architecture: any
+Section: python
+Priority: extra
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, librcsb-core-wrapper0 (= ${binary:Version})
+Suggests: librcsb-core-wrapper0-dbg, librcsb-core-wrapper-doc
+Description: library that exports C++ mmCIF accessors to Python
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This library provides Python bindings for librcsb-core-wrapper.
+
+Package: python-corepywrap-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, librcsb-core-wrapper0 (= ${binary:Version}), python-dbg
+Suggests: librcsb-core-wrapper0-dbg, librcsb-core-wrapper-doc
+Description: library that exports C++ mmCIF accessors to Python (debug version)
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This library provides Python bindings for librcsb-core-wrapper (debugging
+ interpreter).
Added: packages-metadata/l/librcsb-core-wrapper.copyright
===================================================================
--- packages-metadata/l/librcsb-core-wrapper.copyright (rev 0)
+++ packages-metadata/l/librcsb-core-wrapper.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,272 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Core Wrapper
+Upstream-Contact: sw-help at rcsb.rutgers.edu,
+ Vladimir Guranovic <vladimir at rcsb.rutgers.edu>
+Source: http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich, Germany
+License: GPL-3+
+
+Files: regex/*
+Copyright: Copyright 1992, 1993, 1994, 1997 Henry Spencer. All rights reserved.
+License:
+ This software is not subject to any license of the American Telephone
+ and Telegraph Company or of the Regents of the University of California.
+ .
+ Permission is granted to anyone to use this software for any purpose on
+ any computer system, and to alter it and redistribute it, subject
+ to the following restrictions:
+ .
+ 1. The author is not responsible for the consequences of use of this
+ software, no matter how awful, even if they arise from flaws in it.
+ .
+ 2. The origin of this software must not be misrepresented, either by
+ explicit claim or by omission. Since few users ever read sources,
+ credits must appear in the documentation.
+ .
+ 3. Altered versions must be plainly marked as such, and must not be
+ misrepresented as being the original software. Since few users
+ ever read sources, credits must appear in the documentation.
+ .
+ 4. This notice may not be removed or altered.
+
+Files: cctbx/*
+Copyright: Copyright (c) 2006, The Regents of the University of
+ California, through Lawrence Berkeley National Laboratory (subject to
+ receipt of any required approvals from the U.S. Dept. of Energy). All
+ rights reserved.
+License:
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ (1) Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ (2) Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ (3) Neither the name of the University of California, Lawrence Berkeley
+ National Laboratory, U.S. Dept. of Energy nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ .
+ You are under no obligation whatsoever to provide any bug fixes,
+ patches, or upgrades to the features, functionality or performance of
+ the source code ("Enhancements") to anyone; however, if you choose to
+ make your Enhancements available either publicly, or directly to
+ Lawrence Berkeley National Laboratory, without imposing a separate
+ written license agreement for such Enhancements, then you hereby grant
+ the following license: a non-exclusive, royalty-free perpetual license
+ to install, use, modify, prepare derivative works, incorporate into
+ other computer software, distribute, and sublicense such enhancements or
+ derivative works thereof, in binary and source code form.
+
+Files: test/*
+Copyright: John Westbrook
+Comment: http://creativecommons.org/licenses/by/3.0/legalcode
+License: Creative Commons Attribution 3.0 Unported
+ License
+ .
+ THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
+ .
+ BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
+ .
+ 1. Definitions
+ .
+ "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be considered an Adaptation for the purpose of this License. For the avoidance of doubt, where the Work is a musical work, performance or phonogram, the synchronization of the Work in timed-relation with a moving image ("synching") will be considered an Adaptation for the purpose of this License.
+ "Collection" means a collection of literary or artistic works, such as encyclopedias and anthologies, or performances, phonograms or broadcasts, or other works or subject matter other than works listed in Section 1(f) below, which, by reason of the selection and arrangement of their contents, constitute intellectual creations, in which the Work is included in its entirety in unmodified form along with one or more other contributions, each constituting separate and independent works in themselves, which together are assembled into a collective whole. A work that constitutes a Collection will not be considered an Adaptation (as defined above) for the purposes of this License.
+ "Distribute" means to make available to the public the original and copies of the Work or Adaptation, as appropriate, through sale or other transfer of ownership.
+ "Licensor" means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.
+ "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being the person or legal entity who first fixes the sounds of a performance or other sounds; and, (iii) in the case of broadcasts, the organization that transmits the broadcast.
+ "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without words; a cinematographic work to which are assimilated works expressed by a process analogous to cinematography; a work of drawing, painting, architecture, sculpture, engraving or lithography; a photographic work to which are assimilated works expressed by a process analogous to photography; a work of applied art; an illustration, map, plan, sketch or three-dimensional work relative to geography, topography, architecture or science; a performance; a broadcast; a phonogram; a compilation of data to the extent it is protected as a copyrightable work; or a work performed by a variety or circus performer to the extent it is not otherwise considered a literary or artistic work.
+ "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
+ "Publicly Perform" means to perform public recitations of the Work and to communicate to the public those public recitations, by any means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the public by any means or process and the communication to the public of the performances of the Work, including by public digital performance; to broadcast and rebroadcast the Work by any means including signs, sounds or images.
+ "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium.
+ .
+ 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws.
+ .
+ 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:
+ .
+ to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections;
+ to create and Reproduce Adaptations provided that any such Adaptation, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified.";
+ to Distribute and Publicly Perform the Work including as incorporated in Collections; and,
+ to Distribute and Publicly Perform Adaptations.
+ .
+ For the avoidance of doubt:
+ Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;
+ Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and,
+ Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License.
+ .
+ The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved.
+ .
+ 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
+ .
+ You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You must keep intact all notices that refer to this License and to the disclaimer of warranties with every copy of the Work You Distribute or Publicly Perform. When You Distribute or Publicly Perform the Work, You may not impose any effective technological measures on the Work that restrict the ability of a recipient of the Work from You to exercise the rights granted to that recipient under the terms of the License. This Section 4(a) applies to the Work as incorporated in a Collection, but this does not require the Collection apart from the Work itself to be made subject to the terms of this License. If You create a Collection, upon notice from any Licensor You must, to the extent practicable, remove from the Collection any credit as required by Section 4(b), as requested. If You create an Adaptation, upon notice from any Licensor You must, to the extent practicable, remove from the Adaptation any credit as required by Section 4(b), as requested.
+ If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribution ("Attribution Parties") in Licensor's copyright notice, terms of service or by other reasonable means, the name of such party or parties; (ii) the title of the Work if supplied; (iii) to the extent reasonably practicable, the URI, if any, that Licensor specifies to be associated with the Work, unless such URI does not refer to the copyright notice or licensing information for the Work; and (iv) , consistent with Section 3(b), in the case of an Adaptation, a credit identifying the use of the Work in the Adaptation (e.g., "French translation of the Work by Original Author," or "Screenplay based on original Work by Original Author"). The credit required by this Section 4 (b) may be implemented in any reasonable manner; provided, however, that in the case of a Adaptation or Collection, at a minimum such credit will appear, if a credit for all contributing authors of the Adaptation or Collection appears, then as part of these credits and in a manner at least as prominent as the credits for the other contributing authors. For the avoidance of doubt, You may only use the credit required by this Section for the purpose of attribution in the manner set out above and, by exercising Your rights under this License, You may not implicitly or explicitly assert or imply any connection with, sponsorship or endorsement by the Original Author, Licensor and/or Attribution Parties, as appropriate, of You or Your use of the Work, without the separate, express prior written permission of the Original Author, Licensor and/or Attribution Parties.
+ Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to the Work which would be prejudicial to the Original Author's honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any exercise of the right granted in Section 3(b) of this License (the right to make Adaptations) would be deemed to be a distortion, mutilation, modification or other derogatory action prejudicial to the Original Author's honor and reputation, the Licensor will waive or not assert, as appropriate, this Section, to the fullest extent permitted by the applicable national law, to enable You to reasonably exercise Your right under Section 3(b) of this License (right to make Adaptations) but not otherwise.
+ .
+ 5. Representations, Warranties and Disclaimer
+ .
+ UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO SUCH EXCLUSION MAY NOT APPLY TO YOU.
+ .
+ 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+ .
+ 7. Termination
+ .
+ This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
+ Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above.
+ .
+ 8. Miscellaneous
+ .
+ Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.
+ Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License.
+ If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.
+ No term or provision of this License shall be deemed waived and no breach consented to unless such waiver or consent shall be in writing and signed by the party to be charged with such waiver or consent.
+ This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any communication from You. This License may not be modified without the mutual written agreement of the Licensor and You.
+ The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take effect in the relevant jurisdiction in which the License terms are sought to be enforced according to the corresponding provisions of the implementation of those treaty provisions in the applicable national law. If the standard suite of rights granted under applicable copyright law includes additional rights not granted under this License, such additional rights are deemed to be included in the License; this License is not intended to restrict the license of any rights under applicable law.
+
+Files: *
+Copyright: RUTGERS
+License: RUTGERS RCSB PDB SOFTWARE LICENSE AGREEMENT
+
+License: RUTGERS RCSB PDB SOFTWARE LICENSE AGREEMENT
+ RCSB PDB SOFTWARE LICENSE AGREEMENT
+ .
+ BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING
+ THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE
+ SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS
+ BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT
+ AGREE TO ALL OF THE TERMS OF THIS AGREEMENT
+ THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE.
+ .
+ 1. LICENSE AGREEMENT
+ .
+ This is a license between you ("Licensee") and the Protein Data Bank (PDB)
+ at Rutgers, The State University of New Jersey (hereafter referred to
+ as "RUTGERS"). The software is owned by RUTGERS and protected by
+ copyright laws, and some elements are protected by laws governing
+ trademarks, trade dress and trade secrets, and may be protected by
+ patent laws.
+ .
+ 2. LICENSE GRANT
+ .
+ RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free
+ perpetual license to install, use, modify, prepare derivative works,
+ incorporate into other computer software, and distribute in binary
+ and source code format, or any derivative work thereof, together with
+ any associated media, printed materials, and on-line or electronic
+ documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"),
+ subject to the following terms and conditions: (i) any distribution
+ of the SOFTWARE shall bind the receiver to the terms and conditions
+ of this Agreement; (ii) any distribution of the SOFTWARE in modified
+ form shall clearly state that the SOFTWARE has been modified from
+ the version originally obtained from RUTGERS.
+ .
+ 2. COPYRIGHT; RETENTION OF RIGHTS.
+ .
+ The above license grant is conditioned on the following: (i) you must
+ reproduce all copyright notices and other proprietary notices on any
+ copies of the SOFTWARE and you must not remove such notices; (ii) in
+ the event you compile the SOFTWARE, you will include the copyright
+ notice with the binary in such a manner as to allow it to be easily
+ viewable; (iii) if you incorporate the SOFTWARE into other code, you
+ must provide notice that the code contains the SOFTWARE and include
+ a copy of the copyright notices and other proprietary notices. All
+ copies of the SOFTWARE shall be subject to the terms of this Agreement.
+ .
+ 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS
+ .
+ RUTGERS is under no obligation whatsoever to: (i) provide maintenance
+ or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches,
+ or upgrades to the features, functionality or performance of the
+ SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS
+ or third parties. If, in its sole discretion, RUTGERS makes an
+ Enhancement available to you and RUTGERS does not separately enter
+ into a written license agreement with you relating to such bug fix,
+ patch or upgrade, then it shall be deemed incorporated into the SOFTWARE
+ and subject to this Agreement. You are under no obligation whatsoever
+ to provide any Enhancements to RUTGERS or the public that you may
+ develop over time; however, if you choose to provide your Enhancements
+ to RUTGERS, or if you choose to otherwise publish or distribute your
+ Enhancements, in source code form without contemporaneously requiring
+ end users or RUTGERS to enter into a separate written license agreement
+ for such Enhancements, then you hereby grant RUTGERS a non-exclusive,
+ royalty-free perpetual license to install, use, modify, prepare
+ derivative works, incorporate into the SOFTWARE or other computer
+ software, distribute, and sublicense your Enhancements or derivative
+ works thereof, in binary and source code form.
+ .
+ 4. FEES. There is no license fee for the SOFTWARE. If Licensee
+ wishes to receive the SOFTWARE on media, there may be a small charge
+ for the media and for shipping and handling. Licensee is
+ responsible for any and all taxes.
+ .
+ 5. TERMINATION. Without prejudice to any other rights, Licensor
+ may terminate this Agreement if Licensee breaches any of its terms
+ and conditions. Upon termination, Licensee shall destroy all
+ copies of the SOFTWARE.
+ .
+ 6. PROPRIETARY RIGHTS. Title, ownership rights, and intellectual
+ property rights in the Product shall remain with RUTGERS. Licensee
+ acknowledges such ownership and intellectual property rights and will
+ not take any action to jeopardize, limit or interfere in any manner
+ with RUTGERS' ownership of or rights with respect to the SOFTWARE.
+ The SOFTWARE is protected by copyright and other intellectual
+ property laws and by international treaties. Title and related
+ rights in the content accessed through the SOFTWARE is the property
+ of the applicable content owner and is protected by applicable law.
+ The license granted under this Agreement gives Licensee no rights to such
+ content.
+ .
+ 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF
+ CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF
+ ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT
+ IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE
+ OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND
+ PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE
+ SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT
+ LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR.
+ THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF
+ THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER
+ EXCEPT UNDER THIS DISCLAIMER.
+ .
+ 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY
+ APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY
+ INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+ OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING,
+ WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK
+ STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL
+ OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE
+ POSSIBILITY THEREOF.
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
Added: packages-metadata/l/libsort-key-top-perl.control
===================================================================
--- packages-metadata/l/libsort-key-top-perl.control (rev 0)
+++ packages-metadata/l/libsort-key-top-perl.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,27 @@
+Source: libsort-key-top-perl
+Section: perl
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libsort-key-top-perl/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libsort-key-top-perl/trunk/
+Homepage: http://search.cpan.org/dist/Sort-Key-Top/
+
+Package: libsort-key-top-perl
+Architecture: any
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}
+Description: Perl module to select and sort top n elements of a list
+ The functions available from this module select the top n elements from a
+ list using several common orderings and custom key extraction procedures.
+ .
+ They are all variations around 'keytopsort { CALC_KEY($_) } $n => @data;'.
+ .
+ In array context, this function calculates the ordering key for every element
+ in @data using the expression inside the block. Then it selects and orders
+ the $n elements with the lower keys when compared lexicographically.
+ .
+ In scalar context, the value returned by the functions on this module is the
+ cutoff value allowing to select nth element from the array.
Added: packages-metadata/l/libsort-key-top-perl.copyright
===================================================================
--- packages-metadata/l/libsort-key-top-perl.copyright (rev 0)
+++ packages-metadata/l/libsort-key-top-perl.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,46 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Sort::Key::Top
+Upstream-Contact: Salvador Fandiño <sfandino at yahoo.com>
+Source: http://search.cpan.org/~salva/Sort-Key-Top-0.06/lib/Sort/Key/Top.pm
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-3.0+
+
+Files: *
+Copyright: 2006-2008, 2011 by Salvador Fandiño <sfandino at yahoo.com>
+License: Artistic or GPL-1+
+
+License: Artistic
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic'.
+
+License: GPL-1+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 1, or (at your option)
+ any later version.
+ .
+ On Debian systems, the complete text of version 1 of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-1'.
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
Added: packages-metadata/n/ncbi-seg.control
===================================================================
--- packages-metadata/n/ncbi-seg.control (rev 0)
+++ packages-metadata/n/ncbi-seg.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,36 @@
+Source: ncbi-seg
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8), dh-autoreconf
+Standards-Version: 3.9.3
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seg/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seg/trunk/
+DM-Upload-Allowed: yes
+Homepage: ftp://ftp.ncbi.nih.gov/pub/seg/seg/
+
+Package: ncbi-seg
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: tool to mask segments of low compositional complexity in amino acid sequences
+ ncbi-seg (a.k.a. SEG) is a program for identifying and masking segments of
+ low compositional complexity in amino acid sequences.
+ .
+ ncbi-seg divides sequences into contrasting segments of low-complexity and
+ high-complexity. Low-complexity segments defined by the
+ algorithm represent "simple sequences" or "compositionally-biased regions".
+ .
+ This program is inappropriate for masking nucleotide sequences and, in fact,
+ may strip some nucleotide ambiguity codes from nt. sequences as they are being
+ read.
+
+Package: ncbi-seg-dbg
+Section: debug
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ncbi-seg (= ${binary:Version})
+Description: debug symbols for ncbi-seg
+ ncbi-seg (a.k.a. SEG) is a program for identifying and masking segments of
+ low compositional complexity in amino acid sequences.
+ .
+ This package contains detached debug symbols for ncbi-seg.
Added: packages-metadata/n/ncbi-seg.copyright
===================================================================
--- packages-metadata/n/ncbi-seg.copyright (rev 0)
+++ packages-metadata/n/ncbi-seg.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,54 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: seg
+Upstream-Contact: John Wootton <wootton at ncbi.nlm.nih.gov>
+Source: ftp://ftp.ncbi.nih.gov/pub/seg/seg/
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-3+
+
+Files: *
+Copyright: public-domain
+License: public-domain
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the authors' official duties as United States Government employees and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite the authors in any work or product based on this material.
+ .
+ Authors: John C. Wootton, Scott Federhen
+ National Center For Biotechnology Information
+ National Library of Medicine
+ National Institutes of Health
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
Added: packages-metadata/n/ncbi-seg.upstream
===================================================================
--- packages-metadata/n/ncbi-seg.upstream (rev 0)
+++ packages-metadata/n/ncbi-seg.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,9 @@
+Reference:
+ Author: John C. Wootton and Scott Federhen
+ Title: 'Statistics of local complexity in amino acid sequences and sequence databases.'
+ Journal: 'Computers & Chemistry'
+ Year: 1993
+ Volume: 17
+ Pages: 149-163
+ DOI: 10.1016/0097-8485(93)85006-X
+ URL: http://www.sciencedirect.com/science/article/pii/009784859385006X
Added: packages-metadata/n/norsnet.control
===================================================================
--- packages-metadata/n/norsnet.control (rev 0)
+++ packages-metadata/n/norsnet.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,31 @@
+Source: norsnet
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Christian Mertes <mertes at in.tum.de>, Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8)
+Standards-Version: 3.9.3
+Homepage: https://www.rostlab.org/owiki/index.php/Norsnet
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/norsnet/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/norsnet/trunk/
+DM-Upload-Allowed: yes
+
+Package: norsnet
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, profnet-norsnet
+Recommends: blast2, librg-utils-perl, pp-popularity-contest, profphd, profbval
+Description: tool to identify unstructured loops in proteins
+ NORSnet can distinguish between very long contiguous segments with
+ non-regular secondary structure (NORS regions) and well-folded proteins.
+ .
+ NORSnet was trained on predicted information rather than on experimental data.
+ This allows NORSnet to reach into regions in sequence space that are not
+ covered by specialized disorder predictors. One disadvantage of this approach
+ is that it is not optimal for the identification of the "average" disordered
+ region.
+ .
+ NORSnet takes the following input, further described on norsnet(1):
+ * a protein sequence in a FASTA file
+ * secondary structure and solvent accessibility prediction by prof(1)
+ * an HSSP file
+ * flexible/rigid residues prediction by profbval(1)
Added: packages-metadata/n/norsnet.copyright
===================================================================
--- packages-metadata/n/norsnet.copyright (rev 0)
+++ packages-metadata/n/norsnet.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,62 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: norsnet
+Upstream-Contact: A. Schlessinger <avnersch at gmail.com>
+Source: ftp://rostlab.org/norsnet/
+
+Files: examples/cad23-fil.rdbProf
+Copyright: Burkhard Rost, CUBIC NYC / LION Heidelberg
+License: GPL-2.0+
+Comment:
+ License is not indicated in this file, only copyright.
+ Therefore the license here is that of the producing program 'profphd'.
+
+Files: debian/*
+Copyright: 2009 Guy Yachdav <gyachdav at rostlab.org>
+ 2012 Laszlo Kajan <lkajan at rostlab.org>
+ 2012 Christian Mertes <mertes at in.tum.de>
+License: GPL-3+
+
+Files: *
+Copyright: 2007 Avner Schlessinger <avnersch at gmail.com>
+ 2007 Jinfeng Liu <jinfeng.liu at gmail.com>
+ 2007 Burkhard Rost <rost at rostlab.org>
+License: GPL-3+
+
+License: GPL-2.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: GPL-3+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULA
+ PURPOSE. See the GNU General Public License for mor
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
Added: packages-metadata/n/norsnet.upstream
===================================================================
--- packages-metadata/n/norsnet.upstream (rev 0)
+++ packages-metadata/n/norsnet.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,12 @@
+Name: norsnet
+Reference:
+ - Author: Avner Schlessinger and Jinfeng Liu and Burkhard Rost
+ Title: 'Natively unstructured loops differ from other loops.'
+ Journal: PLoS Comput Biol.
+ Volume: 3
+ Pages: e140
+ Year: 2007
+ URL: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030140
+ eprint: http://www.ploscompbiol.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0030140&representation=PDF
+ PMID: 17658943
+ DOI: 10.1371/journal.pcbi.0030140
Added: packages-metadata/n/norsp.control
===================================================================
--- packages-metadata/n/norsp.control (rev 0)
+++ packages-metadata/n/norsp.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,30 @@
+Source: norsp
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>, Eva Reisinger <e.reisinger at gmx.net>
+Build-Depends: debhelper (>= 8)
+Standards-Version: 3.9.3
+Homepage: https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/norsp/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/norsp/trunk/
+DM-Upload-Allowed: yes
+
+Package: norsp
+Architecture: all
+Depends: ${misc:Depends}, perl
+Recommends: blast2, librg-utils-perl, pp-popularity-contest, profphd, ncoils (>= 2002-3)
+Description: predictor of non-regular secondary structure
+ NORSp is a publicly available predictor for disordered regions in proteins.
+ Specifically, it predicts long regions with no regular secondary structure.
+ Upon submission of a protein sequence, NORSp analyses the protein about its
+ secondary structure, the presence of transmembrane helices and coiled-coils.
+ It then returns the presence and position of disordered regions.
+ .
+ NORSp can be useful for biologists in several ways. For example,
+ crystallographers can check whether their proteins contain NORS regions and
+ make the decision about whether to proceed with the experiments since NORS
+ proteins may be difficult to crystallise, as demonstrated by the their low
+ occurrence in PDB. Biologists interested in protein structure-function
+ relationship may also find it interesting to verify whether the
+ protein-protein interaction sites coincide with NORS regions.
Added: packages-metadata/n/norsp.copyright
===================================================================
--- packages-metadata/n/norsp.copyright (rev 0)
+++ packages-metadata/n/norsp.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,33 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: norsp
+Upstream-Contact: Guy Yachdav <gyachdav at rostlab.org>
+Source: ftp://rostlab.org/norsp/
+
+Files: debian/*
+Copyright: 2010 Guy Yachdav <gyachdav at rostlab.org>
+ 2012 Laszlo Kajan <lkajan at rostlab.org>
+ 2012 Eva Reisinger <e.reisinger at gmx.net>
+License: GPL-3+
+
+Files: *
+Copyright: 2003 Jinfeng Liu <jinfeng.liu at gmail.com>
+ 2003 Burkhard Rost
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
Added: packages-metadata/n/norsp.upstream
===================================================================
--- packages-metadata/n/norsp.upstream (rev 0)
+++ packages-metadata/n/norsp.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,13 @@
+Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=norsp
+Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=norsp
+Reference:
+ Author: Jinfeng Liu and Burkhard Rost
+ Title: 'NORSp: Predictions of long regions without regular secondary structure.'
+ Journal: Nucleic Acids Res
+ Year: 2003
+ Volume: 31
+ Number: 13
+ Pages: 3833-3835
+ PMID: 12824431
+ URL: http://nar.oxfordjournals.org/content/31/13/3833.long
+ Eprint: http://nar.oxfordjournals.org/content/31/13/3833.full.pdf
Added: packages-metadata/o/oldsys-preseed.control
===================================================================
--- packages-metadata/o/oldsys-preseed.control (rev 0)
+++ packages-metadata/o/oldsys-preseed.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,18 @@
+Source: oldsys-preseed
+Section: debian-installer
+Priority: optional
+Maintainer: Debian Install System Team <debian-boot at lists.debian.org>
+Uploaders: Martin Michlmayr <tbm at cyrius.com>, Christian Perrier <bubulle at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), devio
+Vcs-Browser: http://git.debian.org/?p=d-i/oldsys-preseed.git
+Vcs-Git: git://git.debian.org/d-i/oldsys-preseed.git
+
+Package: oldsys-preseed
+Package-Type: udeb
+Architecture: any
+Depends: ${depends}
+Description: Preseed debian-installer from an existing device
+ This udeb is used to preseed debian-installer from information already
+ found on a device, such as the network configuration from an existing
+ Unix installation or from flash on some embedded devices.
+
Added: packages-metadata/o/oldsys-preseed.copyright
===================================================================
--- packages-metadata/o/oldsys-preseed.copyright (rev 0)
+++ packages-metadata/o/oldsys-preseed.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,27 @@
+This is oldsys-preseed, written and maintained by:
+ Martin Michlmayr <tbm at cyrius.com>
+
+oldsys-preseed has been written for the debian-installer (d-i).
+
+The original source can always be found at:
+ ftp://ftp.debian.org/dists/unstable/main/source/
+
+Copyright (C) 2005, 2006, 2008, 2009 Martin Michlmayr <tbm at cyrius.com>
+Copyright (C) 2008 Matthew Palmer <mpalmer at debian.org>
+Copyright (C) 2009 Stephen Gran <sgran at debian.org>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License with
+ the Debian GNU/Linux distribution in file /usr/share/common-licenses/GPL;
+ if not, write to the Free Software Foundation, Inc., 51 Franklin St,
+ Fifth Floor, Boston, MA 02110-1301 USA
+
Added: packages-metadata/p/predictnls.control
===================================================================
--- packages-metadata/p/predictnls.control (rev 0)
+++ packages-metadata/p/predictnls.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,20 @@
+Source: predictnls
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Julia Ertl <ertlj at in.tum.de>, Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8), autotools-dev
+Standards-Version: 3.9.3
+Homepage: http://rostlab.org/services/predictNLS/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/predictnls/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/predictnls/trunk/
+DM-Upload-Allowed: yes
+
+Package: predictnls
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Recommends: pp-popularity-contest
+Description: prediction and analysis of protein nuclear localization signals
+ predictnls is a method for the prediction and analysis of protein nuclear
+ localization signals (NLS). In addition to reporting the positions of
+ NLSs found, predictnls also gives short statistics.
Added: packages-metadata/p/predictnls.copyright
===================================================================
--- packages-metadata/p/predictnls.copyright (rev 0)
+++ packages-metadata/p/predictnls.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,35 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: predictnls
+Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
+Source: ftp://rostlab.org/predictnls/
+
+Files: debian/*
+Copyright: 2010, 2012 Laszlo Kajan <lkajan at rostlab.org> Technical University Munich, Germany
+ 2012 Julia Ertl <ertlj at in.tum.de>
+License: GPL-3+
+
+Files: *
+Copyright: 2010 Rajesh Nair <rajnair5 at gmail.com>
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
Added: packages-metadata/p/predictnls.upstream
===================================================================
--- packages-metadata/p/predictnls.upstream (rev 0)
+++ packages-metadata/p/predictnls.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,12 @@
+Reference:
+ - Author: Murat Cokol and Rajesh Nair and Burkhard Rost
+ Title: 'Finding nuclear localization signals.'
+ Journal: EMBO reports
+ Volume: 1
+ Number: 5
+ Pages: 411-415
+ Year: 2000
+ URL: http://www.nature.com/embor/journal/v1/n5/full/embor546.html
+ eprint: http://www.nature.com/embor/journal/v1/n5/pdf/embor546.pdf
+ PMID: 11258480
+ DOI: 10.1093/embo-reports/kvd092
Added: packages-metadata/p/profbval.control
===================================================================
--- packages-metadata/p/profbval.control (rev 0)
+++ packages-metadata/p/profbval.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,35 @@
+Source: profbval
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>, Christof Angermüller <angermue at in.tum.de>
+Build-Depends: debhelper (>= 8), perl
+Standards-Version: 3.9.3
+Homepage: https://www.rostlab.org/owiki/index.php/PROFbval
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/profbval/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/profbval/trunk/
+DM-Upload-Allowed: yes
+
+Package: profbval
+Architecture: all
+Depends: ${perl:Depends}, ${misc:Depends}, profnet-bval
+Recommends: blast2, librg-utils-perl, pp-popularity-contest, profphd
+Description: predictor of flexible/rigid protein residues from sequence
+ PROFbval can be useful for both protein structure and
+ function predictions. For instance, a biologist can locate potentially
+ antigenic determinants by identifying the most flexible residues on the
+ protein surface. Additionally, a crystallographer can locate residues that
+ potentially have high experimental B-values.
+ .
+ PROFbval takes the following input, further described on profbval(1):
+ * a protein sequence in a FASTA file
+ * secondary structure and solvent accessibility prediction by prof(1)
+ * an HSSP file
+ .
+ Background: the mobility of a given residue on the protein surface is related
+ to its functional role.
+ Therefore, identification of extremely rigid or flexible
+ residues on the protein surface is helpful for identifying functionally
+ important residues in proteins. A common measure of atom mobility in proteins
+ is B-value data from x-ray crystallography structures. PROFbval is the first
+ tool to predict normalized backbone B-values from amino-acid sequence.
Added: packages-metadata/p/profbval.copyright
===================================================================
--- packages-metadata/p/profbval.copyright (rev 0)
+++ packages-metadata/p/profbval.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,62 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: profbval
+Upstream-Contact: A. Schlessinger <avnersch at gmail.com>
+Source: ftp://rostlab.org/profbval/
+
+Files: examples/cad23-fil.rdbProf
+Copyright: Burkhard Rost, CUBIC NYC / LION Heidelberg
+License: GPL-2.0+
+Comment:
+ License is not indicated in this file, only copyright.
+ Therefore the license here is that of the producing program 'profphd'.
+
+Files: debian/*
+Copyright: 2009 Guy Yachdav <gyachdav at rostlab.org>
+ 2012 Laszlo Kajan <lkajan at rostlab.org>
+ 2012 Christof Angermüller <angermue at in.tum.de>
+License: GPL-3+
+
+Files: *
+Copyright: 2005, 2006 Avner Schlessinger
+ 2005, 2006 Burhard Rost
+ 2006 Guy Yachdav
+License: GPL-3+
+
+License: GPL-2.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: GPL-3+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 3 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
Added: packages-metadata/p/profbval.upstream
===================================================================
--- packages-metadata/p/profbval.upstream (rev 0)
+++ packages-metadata/p/profbval.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,20 @@
+Name: profbval
+Reference:
+ - Author: Avner Schlessinger and Guy Yachdav and Burkhard Rost
+ Title: 'PROFbval: predict flexible and rigid residues in proteins.'
+ Journal: Bioinformatics
+ Year: 2006
+ Volume: 22
+ Number: 7
+ Pages: 891-3
+ URL: http://www.ncbi.nlm.nih.gov/pubmed?term=PROFbval%3A%20predict%20flexible%20and%20rigid%20residues%20in%20proteins
+ PMID: 16455751
+ - Author: Avner Schlessinger and Burkhard Rost
+ Title: 'Protein flexibility and rigidity predicted from sequence.'
+ Journal: Proteins
+ Year: 2005
+ Volume: 61
+ Number: 1
+ Pages: 115-26
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/16080156
+ PMID: 16080156
Added: packages-metadata/p/profisis.control
===================================================================
--- packages-metadata/p/profisis.control (rev 0)
+++ packages-metadata/p/profisis.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,22 @@
+Source: profisis
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Cedric Staniewski <cedric at gmx.ca>
+Build-Depends: debhelper (>= 8)
+Standards-Version: 3.9.3
+Homepage: https://rostlab.org/owiki/index.php/PROFisis
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profisis/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profisis/trunk/
+
+Package: profisis
+Architecture: all
+Depends: ${misc:Depends}, ${perl:Depends}, libconfig-inifiles-perl, profnet-isis
+Recommends: librg-utils-perl, pp-popularity-contest
+Description: prediction of protein-protein interaction sites from sequence
+ Profisis (ISIS) identifies interacting protein residues in protein-protein
+ interfaces from sequence alone.
+ .
+ The strongest predictions of the method reached over 90% accuracy in a
+ cross-validation experiment.
Added: packages-metadata/p/profisis.copyright
===================================================================
--- packages-metadata/p/profisis.copyright (rev 0)
+++ packages-metadata/p/profisis.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,55 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Yanay Ofran <yanay at ofranlab.org>
+Upstream-Name: profisis
+Source: ftp://rostlab.org/free/
+
+Files: debian/*
+Copyright: 2012 Cedric Staniewski <cedric at gmx.ca>
+ 2010, 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-3.0+
+
+Files: examples/3A1P_A.rdbProf
+Copyright: Burkhard Rost, CUBIC NYC / LION Heidelberg
+License: GPL-2.0+
+Comment:
+ License is not indicated in this file, only copyright.
+ Therefore the license here is that of the producing program 'profphd'.
+
+Files: *
+Copyright: 2006 Yanay Ofran
+ 2006 Burkhard Rost
+License: GPL-3.0+
+
+License: GPL-2.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Added: packages-metadata/p/profisis.upstream
===================================================================
--- packages-metadata/p/profisis.upstream (rev 0)
+++ packages-metadata/p/profisis.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,15 @@
+Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=profisis&component=profisis&resolution=---
+Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=profisis
+Reference:
+ Author: Yanay Ofran and Burkhard Rost
+ Title: "ISIS: interaction sites identified from sequence"
+ Journal: Bioinformatics
+ Year: 2007
+ Volume: 23
+ Number: 2
+ Pages: e13-e16
+ DOI: 10.1093/bioinformatics/btl303
+ PMID: 17237081
+ Type: article
+ URL: http://bioinformatics.oxfordjournals.org/content/23/2/e13.abstract
+ Eprint: http://bioinformatics.oxfordjournals.org/content/23/2/e13.full.pdf+html
Added: packages-metadata/p/python-biom-format.control
===================================================================
--- packages-metadata/p/python-biom-format.control (rev 0)
+++ packages-metadata/p/python-biom-format.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,36 @@
+Source: python-biom-format
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6), python-numpy, cython
+Standards-Version: 3.9.3
+Homepage: http://biom-format.org/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biom-format/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-biom-format/trunk/
+
+Package: python-biom-format
+Architecture: any
+Depends: ${shlibs:Depends}, ${python:Depends}, ${misc:Depends},
+ python-dateutil, python-cogent
+Description: Biological Observation Matrix (BIOM) format
+ The BIOM file format (canonically pronounced biome) is designed to be a
+ general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth
+ Microbiome Project and is a Genomics Standards Consortium candidate
+ project.
+ .
+ The BIOM format is designed for general use in broad areas of
+ comparative -omics. For example, in marker-gene surveys, the primary use
+ of this format is to represent OTU tables: the observations in this case
+ are OTUs and the matrix contains counts corresponding to the number of
+ times each OTU is observed in each sample. With respect to metagenome
+ data, this format would be used to represent metagenome tables: the
+ observations in this case might correspond to SEED subsystems, and the
+ matrix would contain counts corresponding to the number of times each
+ subsystem is observed in each metagenome. Similarly, with respect to
+ genome data, this format may be used to represent a set of genomes: the
+ observations in this case again might correspond to SEED subsystems, and
+ the counts would correspond to the number of times each subsystem is
+ observed in each genome.
Added: packages-metadata/p/python-biom-format.copyright
===================================================================
--- packages-metadata/p/python-biom-format.copyright (rev 0)
+++ packages-metadata/p/python-biom-format.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,40 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biom-format.org
+Upstream-Contact: Greg Caporaso <gregcaporaso at gmail.com>
+Source: http://biom-format.org/ -> links to Github download
+Files-Excluded:
+ ._*
+
+Files: *
+Copyright: © 2010-2012 Greg Caporaso <gregcaporaso at gmail.com>
+License: GPL
+Comment: The code is lacking a license statement but the WNPP bug
+ log contains a mail from upstream
+ http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=682199#15
+ confirming GPL license
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPL
+
+License: GPL
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
Added: packages-metadata/p/python-biom-format.upstream
===================================================================
--- packages-metadata/p/python-biom-format.upstream (rev 0)
+++ packages-metadata/p/python-biom-format.upstream 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,10 @@
+Reference:
+ Author: Daniel McDonald and Jose C. Clemente and Justin Kuczynski and Jai R. Rideout and Jesse Stombaugh and Doug Wendel and Andreas Wilke and Susan Huse and John Hufnagle and Folker Meyer and Rob Knight and J. G. Caporaso
+ Title: "The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome"
+ Journal: GigaScience
+ Year: 2012
+ Volume: 1
+ Pages: 7
+ DOI: 10.1186/2047-217X-1-7
+ URL: http://www.gigasciencejournal.com/content/1/1/7
+ eprint: http://www.gigasciencejournal.com/content/pdf/2047-217X-1-7.pdf
Modified: packages-metadata/p/python-markdown.control
===================================================================
--- packages-metadata/p/python-markdown.control 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/p/python-markdown.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -5,20 +5,21 @@
Uploaders: Fredrik Steen <stone at debian.org>, Bernd Zeimetz <bzed at debian.org>,
Dmitry Shachnev <mitya57 at gmail.com>
Build-Depends: debhelper (>= 8), python-all (>= 2.6.6-3~), python3-all (>= 3.1.2-7~),
- python-nose, python3-nose
+ python-nose, python-utidylib, python3-nose
Standards-Version: 3.9.3
-Homepage: http://www.freewisdom.org/projects/python-markdown/
+Homepage: https://github.com/waylan/Python-Markdown
Vcs-Svn: svn://svn.debian.org/python-modules/packages/python-markdown/trunk/
Vcs-Browser: http://anonscm.debian.org/viewvc/python-modules/packages/python-markdown/trunk/
X-Python-Version: >= 2.6
X-Python3-Version: >= 3.1
+XS-Testsuite: autopkgtest
DM-Upload-Allowed: yes
Package: python-markdown
Architecture: all
Depends: ${python:Depends}, ${misc:Depends}
Recommends: python-pygments
-Suggests: python-markdown-doc
+Suggests: python-utidylib, python-markdown-doc
Description: text-to-HTML conversion library/tool (implemented in Python 2)
Markdown is a text-to-HTML conversion tool for web writers. Markdown
allows you to write using an easy-to-read, easy-to-write plain text
Added: packages-metadata/r/r-bioc-biocgenerics.control
===================================================================
--- packages-metadata/r/r-bioc-biocgenerics.control (rev 0)
+++ packages-metadata/r/r-bioc-biocgenerics.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,22 @@
+Source: r-bioc-biocgenerics
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: cdbs, debhelper (>= 9), r-base-dev (>= 2.14.2~20120222)
+Standards-Version: 3.9.3
+Vcs-Browser: http://git.debian.org/?p=debian-med/r-bioc-biocgenerics.git
+Vcs-Git: git://git.debian.org/debian-med/r-bioc-biocgenerics.git
+Homepage: http://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html
+
+Package: r-bioc-biocgenerics
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends}
+Description: generic functions for Bioconductor
+ S4 generic functions needed by many other Bioconductor packages.
+ .
+ Bioconductor provides tools for the analysis and comprehension of
+ high-throughput genomic data. Bioconductor uses the R statistical
+ programming language, and is open source and open development.
Added: packages-metadata/r/r-bioc-biocgenerics.copyright
===================================================================
--- packages-metadata/r/r-bioc-biocgenerics.copyright (rev 0)
+++ packages-metadata/r/r-bioc-biocgenerics.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,194 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BiocGenerics
+Source: http://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.2.0.tar.gz
+
+Files: *
+Copyright: 2010-2012 The Bioconductor Dev Team
+License: Artistic-2.0
+ Preamble
+ .
+ This license establishes the terms under which a given free software Package
+ may be copied, modified, distributed, and/or redistributed. The intent is that
+ the Copyright Holder maintains some artistic control over the development of
+ that Package while still keeping the Package available as open source and free
+ software.
+ .
+ You are always permitted to make arrangements wholly outside of this license
+ directly with the Copyright Holder of a given Package. If the terms of this
+ license do not permit the full use that you propose to make of the Package, you
+ should contact the Copyright Holder and seek a different licensing arrangement.
+ .
+ Definitions
+ .
+ "Copyright Holder" means the individual(s) or organization(s) named in the
+ copyright notice for the entire Package.
+ .
+ "Contributor" means any party that has contributed code or other material to
+ the Package, in accordance with the Copyright Holder's procedures.
+ .
+ "You" and "your" means any person who would like to copy, distribute, or modify
+ the Package.
+ .
+ "Package" means the collection of files distributed by the Copyright Holder,
+ and derivatives of that collection and/or of those files. A given Package may
+ consist of either the Standard Version, or a Modified Version.
+ .
+ "Distribute" means providing a copy of the Package or making it accessible to
+ anyone else, or in the case of a company or organization, to others outside of
+ your company or organization.
+ .
+ "Distributor Fee" means any fee that you charge for Distributing this Package
+ or providing support for this Package to another party. It does not mean
+ licensing fees.
+ .
+ "Standard Version" refers to the Package if it has not been modified, or has
+ been modified only in ways explicitly requested by the Copyright Holder.
+ .
+ "Modified Version" means the Package, if it has been changed, and such changes
+ were not explicitly requested by the Copyright Holder.
+ .
+ "Original License" means this Artistic License as Distributed with the Standard
+ Version of the Package, in its current version or as it may be modified by The
+ Perl Foundation in the future.
+ .
+ "Source" form means the source code, documentation source, and configuration
+ files for the Package.
+ .
+ "Compiled" form means the compiled bytecode, object code, binary, or any other
+ form resulting from mechanical transformation or translation of the Source
+ form.
+ .
+ Permission for Use and Modification Without Distribution
+ .
+ (1) You are permitted to use the Standard Version and create and use Modified
+ Versions for any purpose without restriction, provided that you do not
+ Distribute the Modified Version.
+ .
+ Permissions for Redistribution of the Standard Version
+ .
+ (2) You may Distribute verbatim copies of the Source form of the Standard
+ Version of this Package in any medium without restriction, either gratis or for
+ a Distributor Fee, provided that you duplicate all of the original copyright
+ notices and associated disclaimers. At your discretion, such verbatim copies
+ may or may not include a Compiled form of the Package.
+ .
+ (3) You may apply any bug fixes, portability changes, and other modifications
+ made available from the Copyright Holder. The resulting Package will still be
+ considered the Standard Version, and as such will be subject to the Original
+ License.
+ .
+ Distribution of Modified Versions of the Package as Source
+ .
+ (4) You may Distribute your Modified Version as Source (either gratis or for a
+ Distributor Fee, and with or without a Compiled form of the Modified Version)
+ provided that you clearly document how it differs from the Standard Version,
+ including, but not limited to, documenting any non-standard features,
+ executables, or modules, and provided that you do at least ONE of the
+ following:
+ .
+ (a) make the Modified Version available to the Copyright Holder of the Standard
+ Version, under the Original License, so that the Copyright Holder may include
+ your modifications in the Standard Version.
+ (b) ensure that installation of your Modified Version does not prevent the user
+ installing or running the Standard Version. In addition, the Modified Version
+ must bear a name that is different from the name of the Standard Version.
+ (c) allow anyone who receives a copy of the Modified Version to make the Source
+ form of the Modified Version available to others under
+ (i) the Original License or
+ (ii) a license that permits the licensee to freely copy, modify and
+ redistribute the Modified Version using the same licensing terms that apply to
+ the copy that the licensee received, and requires that the Source form of the
+ Modified Version, and of any works derived from it, be made freely available in
+ that license fees are prohibited but Distributor Fees are allowed.
+ .
+ Distribution of Compiled Forms of the Standard Version or Modified Versions
+ without the Source
+ .
+ (5) You may Distribute Compiled forms of the Standard Version without the
+ Source, provided that you include complete instructions on how to get the
+ Source of the Standard Version. Such instructions must be valid at the time of
+ your distribution. If these instructions, at any time while you are carrying
+ out such distribution, become invalid, you must provide new instructions on
+ demand or cease further distribution. If you provide valid instructions or
+ cease distribution within thirty days after you become aware that the
+ instructions are invalid, then you do not forfeit any of your rights under this
+ license.
+ .
+ (6) You may Distribute a Modified Version in Compiled form without the Source,
+ provided that you comply with Section 4 with respect to the Source of the
+ Modified Version.
+ .
+ Aggregating or Linking the Package
+ .
+ (7) You may aggregate the Package (either the Standard Version or Modified
+ Version) with other packages and Distribute the resulting aggregation provided
+ that you do not charge a licensing fee for the Package. Distributor Fees are
+ permitted, and licensing fees for other components in the aggregation are
+ permitted. The terms of this license apply to the use and Distribution of the
+ Standard or Modified Versions as included in the aggregation.
+ .
+ (8) You are permitted to link Modified and Standard Versions with other works,
+ to embed the Package in a larger work of your own, or to build stand-alone
+ binary or bytecode versions of applications that include the Package, and
+ Distribute the result without restriction, provided the result does not expose
+ a direct interface to the Package.
+ .
+ Items That are Not Considered Part of a Modified Version
+ .
+ (9) Works (including, but not limited to, modules and scripts) that merely
+ extend or make use of the Package, do not, by themselves, cause the Package to
+ be a Modified Version. In addition, such works are not considered parts of the
+ Package itself, and are not subject to the terms of this license.
+ .
+ General Provisions
+ .
+ (10) Any use, modification, and distribution of the Standard or Modified
+ Versions is governed by this Artistic License. By using, modifying or
+ distributing the Package, you accept this license. Do not use, modify, or
+ distribute the Package, if you do not accept this license.
+ .
+ (11) If your Modified Version has been derived from a Modified Version made by
+ someone other than you, you are nevertheless required to ensure that your
+ Modified Version complies with the requirements of this license.
+ .
+ (12) This license does not grant you the right to use any trademark, service
+ mark, tradename, or logo of the Copyright Holder.
+ .
+ (13) This license includes the non-exclusive, worldwide, free-of-charge patent
+ license to make, have made, use, offer to sell, sell, import and otherwise
+ transfer the Package with respect to any patent claims licensable by the
+ Copyright Holder that are necessarily infringed by the Package. If you
+ institute patent litigation (including a cross-claim or counterclaim) against
+ any party alleging that the Package constitutes direct or contributory patent
+ infringement, then this Artistic License to you shall terminate on the date
+ that such litigation is filed.
+ .
+ (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER
+ AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
+ NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW.
+ UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY
+ OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
+
+Files: debian/*
+Copyright: 2012 Charles Plessy <plessy at debian.org>
+ Andreas Tille <tille at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Modified: packages-metadata/r/r-bioc-qvalue.copyright
===================================================================
--- packages-metadata/r/r-bioc-qvalue.copyright 2012-11-05 04:01:19 UTC (rev 2546)
+++ packages-metadata/r/r-bioc-qvalue.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -2,6 +2,8 @@
Upstream-Name: qvalue
Upstream-Contact: John D. Storey <jstorey at u.washington.edu>
Source: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html
+Files-Excluded:
+ manual.pdf
Files: *
Copyright: © 2006-2012 Alan Dabney and John D. Storey
Added: packages-metadata/r/r-cran-genabel.control
===================================================================
--- packages-metadata/r/r-cran-genabel.control (rev 0)
+++ packages-metadata/r/r-cran-genabel.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,33 @@
+Source: r-cran-genabel
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 8), cdbs, r-base-dev (>= 2.10), r-cran-mass, r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genabel/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-genabel/trunk/
+Homepage: http://www.genabel.org/
+
+Package: r-cran-genabel
+Architecture: any
+Depends: ${shlibs:Depends}, ${R:Depends}, r-cran-mass
+Suggests: r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue
+Provides: r-other-genabel
+Conflicts: r-other-genabel
+Replaces: r-other-genabel
+Description: GNU R package for genome-wide SNP association analysis
+ The package offers the R library GenABEL for the hunt of genetic contributions
+ to a disease (or any other pheonypical trait) by so called genome-wide
+ association analysis. Additional input commonly comes from DNA mircoarray
+ experiments, performed on every individual, that determine differences
+ (polymorphisms) in the population. GenABEL finds associations between
+ quantitative or binary traits and single-nucleiotide polymorphisms
+ (SNPs).
+ .
+ When publishing work based to which this package has contributed please
+ cite: Yurii S. Aulchenko, Stephan Ripke, Aaron Isaacs, Cornelia M. van Duijn
+ (2007) "GenABEL: an R library for genome-wide association analysis"
+ Bioinformatics 2007 23(10):1294-1296.
Added: packages-metadata/v/vobcopy.control
===================================================================
--- packages-metadata/v/vobcopy.control (rev 0)
+++ packages-metadata/v/vobcopy.control 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,22 @@
+Source: vobcopy
+Section: utils
+Priority: optional
+Maintainer: Stephen Birch <sgbirch at imsmail.org>
+Uploaders: Barak A. Pearlmutter <bap at debian.org>
+Build-Depends: debhelper (>= 9), dh-autoreconf, libdvdread-dev
+Standards-Version: 3.9.4
+Homepage: http://vobcopy.org
+Vcs-Git: git://git.debian.org/git/collab-maint/vobcopy.git
+Vcs-Browser: http://git.debian.org/?p=collab-maint/vobcopy.git
+
+Package: vobcopy
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Tool to copy DVD VOBs to hard disk
+ Copies DVD .vob files to harddisk and merges them into file(s)
+ with the name extracted from the DVD. Checks for sufficient free space
+ on the destination drive and compares the copied size to the size on DVD
+ in case something went wrong.
+ .
+ Can also mirror the DVD movie content and copy single
+ specified files.
Added: packages-metadata/v/vobcopy.copyright
===================================================================
--- packages-metadata/v/vobcopy.copyright (rev 0)
+++ packages-metadata/v/vobcopy.copyright 2012-11-06 04:01:25 UTC (rev 2547)
@@ -0,0 +1,27 @@
+This package was debianized by Philippe Normand (phil) <sweafty at free.fr> on
+Mon, 15 Jul 2002 18:27:23 +0200. Debian maintenance of the package was taken
+over on Feb 7, 2004 by Stephen Birch <sgbirch at imsmail.org>.
+
+Upstream location: http://vobcopy.org
+Upstream Author: Robos <robos at muon.de>
+
+This software is copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007 Robos
+<robos at muon.de>, Philippe Normand, Stephen Birch, and lots of contribution and
+cleanup from rosenauer at users.sourceforge.net.
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; version 2 dated June, 1991.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston,
+ MA 02110-1301, USA.
+
+On Debian GNU/Linux systems, the complete text of the GNU General
+Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
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