[Collab-qa-commits] r2631 - in packages-metadata: c m n

Sat Mar 2 03:58:54 UTC 2013

Author: plessy
Date: 2013-03-02 03:58:53 +0000 (Sat, 02 Mar 2013)
New Revision: 2631

Added:
   packages-metadata/c/cdbfasta.control
   packages-metadata/c/cdbfasta.copyright
   packages-metadata/m/macs.control
   packages-metadata/m/macs.copyright
Modified:
   packages-metadata/n/nwchem.upstream
Log:
Daily automatic umegaya push

Added: packages-metadata/c/cdbfasta.control
===================================================================

--- packages-metadata/c/cdbfasta.control	                        (rev 0)
+++ packages-metadata/c/cdbfasta.control	2013-03-02 03:58:53 UTC (rev 2631)
@@ -0,0 +1,21 @@
+Source: cdbfasta
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 9), zlib1g-dev, help2man
+Standards-Version: 3.9.4
+Homepage: http://cdbfasta.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cdbfasta/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cdbfasta/trunk/
+
+Package: cdbfasta
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Constant DataBase indexing and retrieval tools for multi-FASTA files
+ CDB (Constant DataBase) can be used for creating indices for quick
+ retrieval of any particular sequences from large multi-FASTA files.
+ It has the option to compress data records in order to save space.

Added: packages-metadata/c/cdbfasta.copyright
===================================================================
--- packages-metadata/c/cdbfasta.copyright	                        (rev 0)
+++ packages-metadata/c/cdbfasta.copyright	2013-03-02 03:58:53 UTC (rev 2631)
@@ -0,0 +1,35 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cdbfasta
+Upstream-Contact: Geo Pertea <geo.pertea at gmail.com>,
+Source: http://sourceforge.net/projects/cdbfasta/files/
+
+Files: *
+Copyright: © 2002-2010 Geo Pertea <geo.pertea at gmail.com>,
+                       Valentin Antonescu <valduboisvert at yahoo.com>
+                       The Institute for Genomic Research
+License: PD
+ Date: Mon, 17 Dec 2012 11:26:54 -0500
+ From: Geo <geo.pertea at gmail.com>
+ To: andreas at an3as.eu
+ CC: valentin antonescu <valduboisvert at yahoo.com>
+ Subject: Re: Fwd: Please forward to Geo Pertea: What exat license for cdbfasta?
+ .
+ Hi Andreas,
+ I don't think about the licensing issue much and this may be related to 
+ the fact that the cdbfasta code if heavily based on Daniel J. Bernstein 
+ <http://en.wikipedia.org/wiki/Daniel_J._Bernstein>'s cdb source code 
+ which has been notably license-free 
+ <http://en.wikipedia.org/wiki/License-free_software>. However, since DJB 
+ released his individual source code files to public domain we also 
+ consider the whole cdbfasta code to be public domain,  free and open 
+ source software.
+ .
+ Thanks,
+ --geo
+
+Files: debian/*
+Copyright: © 2010 Steffen Moeller <moeller at debian.org>
+           © 2012 Andreas Tille <tille at debian.org>
+License: GPL-3
+ 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/m/macs.control
===================================================================
--- packages-metadata/m/macs.control	                        (rev 0)
+++ packages-metadata/m/macs.control	2013-03-02 03:58:53 UTC (rev 2631)
@@ -0,0 +1,28 @@
+Source: macs
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+ H. Soon Gweon <hyugwe at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9), cython (>= 0.15), python-dev (>= 2.7), help2man,
+ python-numpy
+Standards-Version: 3.9.4
+X-Python-Version: >=2.7
+Homepage: https://github.com/taoliu/MACS/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/macs/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/macs/trunk/
+
+Package: macs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy
+Description: Model-based Analysis of ChIP-Seq on short reads sequencers
+ MACS empirically models the length of the sequenced ChIP fragments, which 
+ tends to be shorter than sonication or library construction size estimates, 
+ and uses it to improve the spatial resolution of predicted binding sites. 
+ MACS also uses a dynamic Poisson distribution to effectively capture local 
+ biases in the genome sequence, allowing for more sensitive and robust 
+ prediction. MACS compares favorably to existing ChIP-Seq peak-finding 
+ algorithms, is publicly available open source, and can be used for ChIP-Seq 
+ with or without control samples.

Added: packages-metadata/m/macs.copyright
===================================================================
--- packages-metadata/m/macs.copyright	                        (rev 0)
+++ packages-metadata/m/macs.copyright	2013-03-02 03:58:53 UTC (rev 2631)
@@ -0,0 +1,19 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MACS
+Upstream-Contact: Tao Liu <vladimir.liu at gmail.com>,
+                  Yong Zhang <zy at jimmy.harvard.edu>
+Source: https://github.com/taoliu/MACS/downloads 
+
+Files: *
+Copyright: 2008 Zhang et al.
+License: Artistic
+ The complete text of the Artistic License can be found in 
+ /usr/share/common-licenses/Artistic
+
+Files: debian/*
+Copyright: 2011 Tim Booth <tbooth at ceh.ac.uk>,
+                Andreas Tille <tille at debian.org>
+License: Artistic
+ The complete text of the Artistic License can be found in 
+ /usr/share/common-licenses/Artistic
+

Modified: packages-metadata/n/nwchem.upstream
===================================================================
--- packages-metadata/n/nwchem.upstream	2013-03-01 03:58:51 UTC (rev 2630)
+++ packages-metadata/n/nwchem.upstream	2013-03-02 03:58:53 UTC (rev 2631)
@@ -1,5 +1,5 @@
 Reference:
-  Author: "M. Valiev and E.J. Bylaska and N. Govind and K. Kowalski and T.P. Straatsma and H.J.J. van Dam and D. Wang and J. Nieplocha and E. Apra and T.L. Windus and W.A. de Jong
+  Author: "M. Valiev and E.J. Bylaska and N. Govind and K. Kowalski and T.P. Straatsma and H.J.J. van Dam and D. Wang and J. Nieplocha and E. Apra and T.L. Windus and W.A. de Jong"
   Title: "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations"
   Journal: Comput. Phys. Commun.
   Year: 2010


