[med-svn] r8953 - in trunk/packages/cd-hit/trunk: . debian debian/patches debian/source
Andreas Tille
tille at alioth.debian.org
Wed Dec 14 15:45:03 UTC 2011
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+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 <liwz at sdsc.edu>
+Source: http://code.google.com/p/cdhit/downloads/list
+
+Files: *
+Copyright: © 2009-2011 Weizhong Li <liwz at sdsc.edu>
+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 <tille at debian.org>
+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 <tille at debian.org>
+# 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 <liwz at sdsc.edu>
+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
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