Author: tille Date: 2011-12-14 15:45:03 +0000 (Wed, 14 Dec 2011) New Revision: 8953
Added: trunk/packages/cd-hit/trunk/debian/ trunk/packages/cd-hit/trunk/debian/changelog trunk/packages/cd-hit/trunk/debian/compat trunk/packages/cd-hit/trunk/debian/control trunk/packages/cd-hit/trunk/debian/copyright trunk/packages/cd-hit/trunk/debian/dirs trunk/packages/cd-hit/trunk/debian/links trunk/packages/cd-hit/trunk/debian/patches/ trunk/packages/cd-hit/trunk/debian/patches/fix_makefile_clean_target.patch trunk/packages/cd-hit/trunk/debian/patches/series trunk/packages/cd-hit/trunk/debian/rules trunk/packages/cd-hit/trunk/debian/source/ trunk/packages/cd-hit/trunk/debian/source/format trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml trunk/packages/cd-hit/trunk/debian/watch Log: Commit packaging stuff for cd-hit Added: trunk/packages/cd-hit/trunk/debian/changelog =================================================================== --- trunk/packages/cd-hit/trunk/debian/changelog (rev 0) +++ trunk/packages/cd-hit/trunk/debian/changelog 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,5 @@ +cd-hit (4.5.6-1) experimental; urgency=low + + * Initial release + + -- Andreas Tille <[email protected]> Wed, 14 Dec 2011 14:39:32 +0100 Added: trunk/packages/cd-hit/trunk/debian/compat =================================================================== --- trunk/packages/cd-hit/trunk/debian/compat (rev 0) +++ trunk/packages/cd-hit/trunk/debian/compat 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1 @@ +8 Added: trunk/packages/cd-hit/trunk/debian/control =================================================================== --- trunk/packages/cd-hit/trunk/debian/control (rev 0) +++ trunk/packages/cd-hit/trunk/debian/control 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,24 @@ +Source: cd-hit +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Tim Booth <[email protected]>, + Andreas Tille <[email protected]> +DM-Upload-Allowed: yes +Build-Depends: debhelper (>= 8) +Standards-Version: 3.9.2 +Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cd-hit/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cd-hit/trunk/ + +Package: cd-hit +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, +Description: suite of programs designed to quickly group sequences + cd-hit contains a number of programs designed to quickly group + sequences. cd-hit groups proteins into clusters that meet a user-defined + similarity threshold. cd-hit-est is similar to cd-hit, but designed to + group nucleotide sequences (without introns). cd-hit-est-2d is similar + to cd-hit-2d but designed to compare two nucleotide datasets. A number + of other related programs are also in this package. Please see the + cd-hit user manual, also part of this package, for further information. Added: trunk/packages/cd-hit/trunk/debian/copyright =================================================================== --- trunk/packages/cd-hit/trunk/debian/copyright (rev 0) +++ trunk/packages/cd-hit/trunk/debian/copyright 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,28 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: CD-HIT +Upstream-Contact: Weizhong Li <[email protected]> +Source: http://code.google.com/p/cdhit/downloads/list + +Files: * +Copyright: © 2009-2011 Weizhong Li <[email protected]> +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 program. If not, see <http://www.gnu.org/licenses/>. +Comment: 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'. + +Files: debian/* +Copyright: © 2011 Andreas Tille <[email protected]> +License: Same as cd-hit itself (GPL-2) + 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: trunk/packages/cd-hit/trunk/debian/dirs =================================================================== --- trunk/packages/cd-hit/trunk/debian/dirs (rev 0) +++ trunk/packages/cd-hit/trunk/debian/dirs 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1 @@ +/usr/lib/cd-hit Added: trunk/packages/cd-hit/trunk/debian/links =================================================================== --- trunk/packages/cd-hit/trunk/debian/links (rev 0) +++ trunk/packages/cd-hit/trunk/debian/links 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,23 @@ +usr/lib/cd-hit/cd-hit usr/bin/cdhit +usr/lib/cd-hit/cd-hit-2d usr/bin/cdhit-2d +usr/lib/cd-hit/cd-hit-2d-para.pl usr/bin/cd-hit-2d-para +usr/lib/cd-hit/cd-hit-div.pl usr/bin/cd-hit-div +usr/lib/cd-hit/cd-hit-est usr/bin/cdhit-est +usr/lib/cd-hit/cd-hit-est-2d usr/bin/cdhit-est-2d +usr/lib/cd-hit/cd-hit-para.pl usr/bin/cd-hit-para +usr/lib/cd-hit/clstr2tree.pl usr/bin/clstr2tree +usr/lib/cd-hit/clstr_merge_noorder.pl usr/bin/clstr_merge_noorder +usr/lib/cd-hit/clstr_merge.pl usr/bin/clstr_merge +usr/lib/cd-hit/clstr_reduce.pl usr/bin/clstr_reduce +usr/lib/cd-hit/clstr_renumber.pl usr/bin/clstr_renumber +usr/lib/cd-hit/clstr_rev.pl usr/bin/clstr_rev +usr/lib/cd-hit/clstr_sort_by.pl usr/bin/clstr_sort_by +usr/lib/cd-hit/clstr_sort_prot_by.pl usr/bin/clstr_sort_prot_by +usr/lib/cd-hit/make_multi_seq.pl usr/bin/make_multi_seq +## Too generic name, please point your PATH to /usr/lib/cd-hit +# usr/lib/cd-hit/plot_2d.pl usr/bin/plot_2d +# usr/lib/cd-hit/plot_len1.pl usr/bin/plot_len1 +usr/lib/cd-hit/psi-cd-hit-2d-g1.pl usr/bin/psi-cd-hit-2d-g1 +usr/lib/cd-hit/psi-cd-hit-2d.pl usr/bin/psi-cd-hit-2d +usr/lib/cd-hit/psi-cd-hit-local.pl usr/bin/psi-cd-hit-local +usr/lib/cd-hit/psi-cd-hit.pl usr/bin/psi-cd-hit Added: trunk/packages/cd-hit/trunk/debian/patches/fix_makefile_clean_target.patch =================================================================== --- trunk/packages/cd-hit/trunk/debian/patches/fix_makefile_clean_target.patch (rev 0) +++ trunk/packages/cd-hit/trunk/debian/patches/fix_makefile_clean_target.patch 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,11 @@ +--- cd-hit-v4.5.6-2011-09-02.orig/Makefile ++++ cd-hit-v4.5.6-2011-09-02/Makefile +@@ -32,7 +32,7 @@ + all: $(PROGS) + + clean: +- rm *.o $(PROGS) ++ rm -f *.o $(PROGS) + + # programs + Added: trunk/packages/cd-hit/trunk/debian/patches/series =================================================================== --- trunk/packages/cd-hit/trunk/debian/patches/series (rev 0) +++ trunk/packages/cd-hit/trunk/debian/patches/series 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1 @@ +fix_makefile_clean_target.patch Added: trunk/packages/cd-hit/trunk/debian/rules =================================================================== --- trunk/packages/cd-hit/trunk/debian/rules (rev 0) +++ trunk/packages/cd-hit/trunk/debian/rules 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,16 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules for cd-hit +# Andreas Tille <[email protected]> +# GPL + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') + +%: + dh $@ + +override_dh_auto_install: + dh_auto_install -- PREFIX=debian/$(pkg)/usr/lib/cd-hit Property changes on: trunk/packages/cd-hit/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/cd-hit/trunk/debian/source/format =================================================================== --- trunk/packages/cd-hit/trunk/debian/source/format (rev 0) +++ trunk/packages/cd-hit/trunk/debian/source/format 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml =================================================================== --- trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,12 @@ +Contact: Weizhong Li <[email protected]> +DOI: 10.1093/bioinformatics/btl158 +Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ +Name: CD-HIT +PMID: 16731699 +Reference: + author: Weizhong Li, Adam Godzik + title: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. + journal: Bioinformatics + volume: 22 + year: 2006 + URL: http://bioinformatics.oxfordjournals.org/content/22/13/1658.full.pdf+html Added: trunk/packages/cd-hit/trunk/debian/watch =================================================================== --- trunk/packages/cd-hit/trunk/debian/watch (rev 0) +++ trunk/packages/cd-hit/trunk/debian/watch 2011-12-14 15:45:03 UTC (rev 8953) @@ -0,0 +1,2 @@ +version=3 +http://googlecode.debian.net/p/cdhit/cd-hit-v([.\d]+)[-\d]+\.tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
