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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 <[email protected]> -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 <[email protected]> - Oliver Sander <[email protected]> -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 <[email protected]> Debianized-By: Dominique Belhachemi <[email protected]> Debianized-Date: Tue, 24 Jun 2008 20:51:56 +0200 Original-Source: http://www.sofa-framework.org/ -Upstream-Contact: Francois Faure <[email protected]> Files: framework/* Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS @@ -75,3 +75,4 @@ Copyright: 2008, Dominique Belhachemi <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 <[email protected]>, +Copyright: © 2011-2012 William Spooner <[email protected]>, Andreas Tille <[email protected]>, + Thorsten Alteholz <[email protected]> +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". _______________________________________________ Collab-qa-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/collab-qa-commits
