[Collab-qa-commits] r2175 - in packages-metadata: c d i l m p r s t w
Charles Plessy
plessy at alioth.debian.org
Sat Mar 17 04:59:00 UTC 2012
Author: plessy
Date: 2012-03-17 04:59:00 +0000 (Sat, 17 Mar 2012)
New Revision: 2175
Modified:
packages-metadata/c/cufflinks.upstream
packages-metadata/d/dialign-tx.upstream
packages-metadata/i/infernal.upstream
packages-metadata/l/libtfbs-perl.upstream
packages-metadata/m/mafft.upstream
packages-metadata/m/maq.upstream
packages-metadata/p/probalign.upstream
packages-metadata/r/r-cran-rocr.upstream
packages-metadata/s/sofa-apps.copyright
packages-metadata/t/t-coffee.upstream
packages-metadata/t/transtermhp.upstream
packages-metadata/t/treeviewx.upstream
packages-metadata/w/wgs-assembler.copyright
Log:
Manual update after re-scanning the Debian Med repository.
Modified: packages-metadata/c/cufflinks.upstream
===================================================================
--- packages-metadata/c/cufflinks.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/c/cufflinks.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -2,7 +2,7 @@
Homepage: http://cufflinks.cbcb.umd.edu/
Name: Cufflinks
Reference:
- Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
+ Author: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Journal: Nature Biotechnology
DOI: doi:10.1038/nbt.1621
Modified: packages-metadata/d/dialign-tx.upstream
===================================================================
--- packages-metadata/d/dialign-tx.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/d/dialign-tx.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,7 +1,5 @@
Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-Reference-DOI: 10.1186/1748-7188-3-6
Homepage: http://dialign-tx.gobics.de/
-Reference-PMID: 18505568
Name: DIALIGN-T
Reference:
AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard
@@ -14,5 +12,6 @@
PAGES: 6
URL: http://www.almob.org/content/3/1/6
DOI: 10.1186/1748-7188-3-6
+ PMID: 18505568
ISSN: 1748-7188
Watch: http://dialign-tx.gobics.de/download http://dialign-tx.gobics.de/DIALIGN-TX_(.*)\.tar\.gz
Modified: packages-metadata/i/infernal.upstream
===================================================================
--- packages-metadata/i/infernal.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/i/infernal.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,6 +1,4 @@
-Reference-DOI: 10.1093/bioinformatics/btp157
Homepage: http://infernal.janelia.org/
-Reference-PMID: 19307242
Reference:
author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
title: "Infernal 1.0: inference of RNA alignments"
@@ -9,6 +7,7 @@
number: 10
pages: 1335-1337
doi: 10.1093/bioinformatics/btp157
+ PMID: 19307242
year: 2009
URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
Modified: packages-metadata/l/libtfbs-perl.upstream
===================================================================
--- packages-metadata/l/libtfbs-perl.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/l/libtfbs-perl.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,16 +1,17 @@
Contact: Boris.Lenhard at bccs.uib.no
-Reference-DOI: 10.1093/bioinformatics/18.8.1135
Homepage: http://tfbs.genereg.net/
Name: TFBS
-Reference-PMID: 12176838
-Reference-Journal: Bioinformatics
-Reference-Title: >
- TFBS: Computational framework for transcription factor binding site analysis
-Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W.
-Reference-Volume: 18
-Reference-Number: 8
-Reference-Pages: 1135-1136
-Reference-Year: 2002
-Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
+Reference:
+ DOI: 10.1093/bioinformatics/18.8.1135
+ PMID: 12176838
+ Journal: Bioinformatics
+ Title: >
+ TFBS: Computational framework for transcription factor binding site analysis
+ Author: Lenhard, Boris and Wasserman, Wyeth W.
+ Volume: 18
+ Number: 8
+ Pages: 1135-1136
+ Year: 2002
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
Modified: packages-metadata/m/mafft.upstream
===================================================================
--- packages-metadata/m/mafft.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/m/mafft.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,15 +1,16 @@
Contact: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
-Reference-DOI: 10.1093/bib/bbn013
Name: MAFFT
Homepage: http://mafft.cbrc.jp/alignment/software/
-Reference-PMID: 18372315
-Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki
-Reference-Journal: Brief Bioinform
-Reference-Number: 4
-Reference-Pages: 286-298
-Reference-Title: Recent developments in the MAFFT multiple sequence alignment program
-Reference-URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286
-Reference-Volume: 9
-Reference-Year: 2008
+Reference:
+ DOI: 10.1093/bib/bbn013
+ PMID: 18372315
+ Author: Katoh, Kazutaka and Toh, Hiroyuki
+ Journal: Brief Bioinform
+ Number: 4
+ Pages: 286-298
+ Title: Recent developments in the MAFFT multiple sequence alignment program
+ URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286
+ Volume: 9
+ Year: 2008
Watch: |
http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-with-extensions-src.tgz
Modified: packages-metadata/m/maq.upstream
===================================================================
--- packages-metadata/m/maq.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/m/maq.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,10 +1,8 @@
Archive: SourceForge
Contact: Heng Li <lh3 at sanger.ac.uk>
-Reference-DOI: 10.1101/gr.078212.108
FAQ: http://maq.sourceforge.net/faq.shtml
Name: Maq
Homepage: http://maq.sourceforge.net/
-Reference-PMID: 18714091
Reference:
author: Li, Heng and Ruan, Jue and Durbin, Richard
title: Mapping short DNA sequencing reads and calling variants using mapping quality scores
@@ -13,6 +11,7 @@
number: 11
pages: 1851-1858
doi: 10.1101/gr.078212.108
+ PMID: 18714091
year: 2008
URL: http://genome.cshlp.org/content/18/11/1851.abstract
eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html
Modified: packages-metadata/p/probalign.upstream
===================================================================
--- packages-metadata/p/probalign.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/p/probalign.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,11 +1,9 @@
Contact: Usman Roshan <usman at cs.njit.edu>
-Reference-DOI: 10.1093/bioinformatics/btl472
Homepage: http://cs.njit.edu/usman/probalign/
-Reference-PMID: 16954142
Name: Probalign
Reference:
AUTHOR: Usman Roshan, Dennis R. Livesay
- TITILE: >
+ TITLE: >
Probalign: multiple sequence alignment using partition function posterior probabilities
JOURNAL: Bioinformatics
YEAR: 2006
@@ -14,3 +12,5 @@
NUMBER: 22
URL: http://bioinformatics.oxfordjournals.org/content/22/22/2715.short
ISSN: 1460-2059
+ DOI: 10.1093/bioinformatics/btl472
+ PMID: 16954142
Modified: packages-metadata/r/r-cran-rocr.upstream
===================================================================
--- packages-metadata/r/r-cran-rocr.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/r/r-cran-rocr.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,19 +1,19 @@
Contact:
- Tobias Sing <tobias.sing at mpi-sb.mpg.de>
- Oliver Sander <osander at mpi-sb.mpg.de>
-Reference-DOI: 10.1093/bioinformatics/bti623
Gallery: http://rocr.bioinf.mpi-sb.mpg.de/rocr_gallery.html
Homepage: http://rocr.bioinf.mpi-sb.mpg.de
Name: ROCR
-Reference-PMID: 16096348
-Reference: |
+Reference:
author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas
- title: ROCR: visualizing classifier performance in R
+ title: "ROCR: visualizing classifier performance in R"
journal: Bioinformatics
volume: 21
number: 20
pages: 3940-3941
year: 2005
+ PMID: 16096348
+ DOI: 10.1093/bioinformatics/bti623
URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/20/3940
eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/21/20/3940.pdf
Screenshot:
Modified: packages-metadata/s/sofa-apps.copyright
===================================================================
--- packages-metadata/s/sofa-apps.copyright 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/s/sofa-apps.copyright 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,8 +1,8 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Francois Faure <francois.faure at inria.fr>
Debianized-By: Dominique Belhachemi <domibel at debian.org>
Debianized-Date: Tue, 24 Jun 2008 20:51:56 +0200
Original-Source: http://www.sofa-framework.org/
-Upstream-Contact: Francois Faure <francois.faure at inria.fr>
Files: framework/*
Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS
@@ -75,3 +75,4 @@
Copyright: 2008, Dominique Belhachemi <domibel at debian.org>
License: GPL-2+
The Debian packaging is licensed under the GPL, see `/usr/share/common-licenses/GPL-2'
+
Modified: packages-metadata/t/t-coffee.upstream
===================================================================
--- packages-metadata/t/t-coffee.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/t/t-coffee.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,16 +1,17 @@
Contact: Cédric Notredame <cedric.notredame at europe.com>
-Reference-DOI: 10.1006/jmbi.2000.4042
Name: T-Coffee
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-Reference-PMID: 10964570
-Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
-Reference-Journal: Journal of Molecular Biology
-Reference-Number: 1
-Reference-Pages: 205-217
-Reference-Title: >
- T-coffee: a novel method for fast and accurate multiple sequence alignment
-Reference-URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed
-Reference-Volume: 302
-Reference-Year: 2000
+Reference:
+ DOI: 10.1006/jmbi.2000.4042
+ PMID: 10964570
+ Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
+ Journal: Journal of Molecular Biology
+ Number: 1
+ Pages: 205-217
+ Title: >
+ T-coffee: a novel method for fast and accurate multiple sequence alignment
+ URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed
+ Volume: 302
+ Year: 2000
Watch: http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz
Webservice: http://tcoffee.crg.cat/apps/tcoffee/do:regular
Modified: packages-metadata/t/transtermhp.upstream
===================================================================
--- packages-metadata/t/transtermhp.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/t/transtermhp.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,11 +1,11 @@
Contact: Carl Kingsford <carlk at umiacs.umd.edu>
-Reference-DOI: 10.1186/gb-2007-8-2-r22
Homepage: http://transterm.cbcb.umd.edu/
-Reference-PMID: 17313685
Name: TransTermHP
Reference:
AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg
- TITILE: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
+ TITLE: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
JOURNAL: Genome Biology
YEAR: 2007
URL: http://genomebiology.com/2007/8/2/R22/abstract
+ DOI: 10.1186/gb-2007-8-2-r22
+ PMID: 17313685
Modified: packages-metadata/t/treeviewx.upstream
===================================================================
--- packages-metadata/t/treeviewx.upstream 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/t/treeviewx.upstream 2012-03-17 04:59:00 UTC (rev 2175)
@@ -7,7 +7,7 @@
Author: Page, Roderic D. M.
Journal: Comput. Appl. Biosci.
Number: 4
- Page: 357-8
+ Pages: 357-8
Title: >
TreeView: an application to display phylogenetic trees on personal computers
URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
Modified: packages-metadata/w/wgs-assembler.copyright
===================================================================
--- packages-metadata/w/wgs-assembler.copyright 2012-03-17 04:38:27 UTC (rev 2174)
+++ packages-metadata/w/wgs-assembler.copyright 2012-03-17 04:59:00 UTC (rev 2175)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0
Upstream-Name: WGS-Assembler
Upstream-Contact: Brian Walenz
Source: http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/
@@ -13,23 +13,28 @@
R. L. Strausberg, C. A. Saski, D. Lawson,
F. H. Collins, F. C. Kafatos, G. K. Christophides,
S. W. Clifton, E. F. Kirkness and N. J. Besansky
-
License: GPL-2+
+ wgs-assembler 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.
+ .
+ Velvet 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 Velvet; 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 version 2 can be found in "/usr/share/common-licenses/GPL-2".
- wgs-assembler 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.
-
- Velvet 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 Velvet; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
Files: debian/*
-Copyright: © 2011 William Spooner <whs at eaglegenomics.com>,
+Copyright: © 2011-2012 William Spooner <whs at eaglegenomics.com>,
Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+License: GPL-2+
+ On Debian 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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