debian/0000755000000000000000000000000012203227102007155 5ustar debian/doc-base0000644000000000000000000000136111674562404010600 0ustar Document: cd-hit Title: CD-HIT User's Guide Author: Weizhong Li , Limin Fu Abstract: 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. Section: Science/Biology Format: pdf Files: /usr/share/doc/cd-hit/cdhit-user-guide.pdf debian/README.Debian0000644000000000000000000000045711746170103011235 0ustar Cd-hit for Debian ================= Currently cd-hit is built with MPI support. Please drop the Debian Med team a note (or file a bug report using `reportbug cd-hit`) and ask us for supporting an alternative package without MPI. -- Andreas Tille Thu, 26 Apr 2012 07:54:23 +0200 debian/cd-hit.txt0000644000000000000000000000243311674551527011116 0ustar Andreas, The attached is the LaTex source. This is not currently included in the cd-hit release yet. But in the future, we consider to have the LaTex file packaged into cd-hit release. Thanks a lot, let me know if anything is needed. Weizhong, On 12/19/11 8:19 AM, Andreas Tille wrote: > Hi Weizhong, > > On Mon, Dec 19, 2011 at 08:14:15AM -0800, Weizhong Li wrote: > >> Sorry for not getting you back within the weekend. Now I fully under >> the requirement. >> > I wished other upstream authors would answer as fast as you - no need > for sorry at all. > > >> If you are not in hurry, we can create a LaTeX version for this >> release and have it back to you in a day or two. >> > That's a perfectly fine time scale. > > >> Otherwise, you can strip the documentation from the package for now. >> >> I think for both case, we will consider LaTeX document in future >> cd-hit releases. >> > That's perfect. > > Many thanks for your cooperation > > Andreas. > > -- Weizhong Li Ph.D.& Principal Investigator Center for Research in Biological Systems University of California, San Diego 9500 Gilman Drive MC 0446 Atkinson Hall, Room 3113 La Jolla CA 92093-0446 E-mail: weizhong@ucsd.edu, liwz@sdsc.edu www: http://weizhong-lab.ucsd.edu Phone: (858) 534 4143 debian/source/0000755000000000000000000000000012203226575010472 5ustar debian/source/format0000644000000000000000000000001411513054733011676 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000003111746161742010044 0ustar doc/cdhit-user-guide.pdf debian/dirs0000644000000000000000000000002011672134016010043 0ustar /usr/lib/cd-hit debian/copyright0000644000000000000000000000367611744731710011142 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: CD-HIT Upstream-Contact: Weizhong Li Source: http://code.google.com/p/cdhit/downloads/list Files: * Copyright: © 2009-2011 Weizhong Li License: GPL-2 Files: cdhit-user-guide.pdf Copyright: © 2009-2011 Weizhong Li License: GPL-2 Comment: LaTeX source for documentation will be included in future release The author provided the source for the documentation in an archive sended in CC to the Debian Med mailing list. The content is stored in the source package in debian/doc-source for the moment. . Date: Wed, 21 Dec 2011 14:23:00 -0800 From: Weizhong Li To: Andreas Tille CC: Debian Med Project List Subject: Re: Packaging of cd-hit for Debian . Andreas, The attached is the LaTex source. This is not currently included in the cd-hit release yet. But in the future, we consider to have the LaTex file packaged into cd-hit release. Thanks a lot, let me know if anything is needed. Weizhong Files: debian/* Copyright: © 2011 Andreas Tille License: GPL-2 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 . . 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'. debian/upstream0000644000000000000000000000077211745027007010762 0ustar Contact: Weizhong Li Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Name: CD-HIT Reference: author: Weizhong Li and 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 PMID: 16731699 DOI: 10.1093/bioinformatics/btl158 URL: http://bioinformatics.oxfordjournals.org/content/22/13/1658 eprint: http://bioinformatics.oxfordjournals.org/content/22/13/1658.full.pdf+html debian/rules0000755000000000000000000000676312203212144010251 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for cd-hit # Andreas Tille # GPL # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') ver := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/ %: dh $@ override_dh_auto_build: dh_auto_build -- openmp=yes override_dh_installman: mkdir -p $(mandir) help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='quickly group sequences' \ $(CURDIR)/cd-hit | \ sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > $(mandir)/cdhit.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='quickly group sequences, optimised for 454 data' \ $(CURDIR)/cd-hit-454 | \ sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > $(mandir)/cdhit-454.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='quickly group sequences in db1 or db2 format' \ $(CURDIR)/cd-hit-2d | \ sed -e 's/^cd-\(hit-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > $(mandir)/cdhit-2d.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='run CD-HIT algorithm on RNA/DNA sequences' \ $(CURDIR)/cd-hit-est | \ sed -e 's/^cd-\(hit-est \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > $(mandir)/cdhit-est.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \ $(CURDIR)/cd-hit-est-2d | \ sed -e 's/^cd-\(hit-est-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \ > $(mandir)/cdhit-est-2d.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \ $(CURDIR)/cd-hit-2d-para.pl > $(mandir)/cd-hit-2d-para.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \ $(CURDIR)/cd-hit-para.pl > $(mandir)/cd-hit-para.1 # psi-cd-hit.pl is throwing some errors which are fixed using sed help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \ $(CURDIR)/psi-cd-hit.pl | \ sed -e '/^Name "main::.*" used only once:/d' \ > $(mandir)/psi-cd-hit.1 help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ $(CURDIR)/psi-cd-hit-2d.pl > $(mandir)/psi-cd-hit-2d.1 # FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ? help2man --no-info --no-discard-stderr --version-string='$(ver)' \ --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \ $(CURDIR)/psi-cd-hit-2d-g1.pl > $(mandir)/psi-cd-hit-2d-g1.1 # No help output from # cd-hit-div.pl # clstr2tree.pl # clstr_merge.pl # clstr_merge_noorder.pl # clstr_reduce.pl # clstr_renumber.pl # clstr_rev.pl # clstr_sort_by.pl # clstr_sort_prot_by # make_multi_seq # psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors override_dh_auto_install: dh_auto_install -- PREFIX=debian/$(pkg)/usr/lib/cd-hit override_dh_compress: dh_compress --exclude=.pdf debian/patches/0000755000000000000000000000000012203226575010621 5ustar debian/patches/enable_help2man.patch0000644000000000000000000000166712201651256014664 0ustar Author: Andreas Tille LastChanged: Sun, 11 Aug 2013 10:51:30 +0200 Description: Help help2man to run without producing errors --- a/cd-hit-2d-para.pl +++ b/cd-hit-2d-para.pl @@ -55,7 +55,7 @@ while ($arg=shift) { elsif ($arg eq "--Q" ) { $queue = shift; } elsif ($arg eq "--T" ) { $queue_type = shift; } elsif ($arg eq "--R" ) { $restart_in = shift; } - else {$arg_pass .= " $arg "; } + else {$arg_pass .= " $arg " ; $arg_pass .= shift if (shift) } } ($in and $out) || print_usage(); if (not ($seg_no2 >1)) { --- a/cd-hit-para.pl +++ b/cd-hit-para.pl @@ -52,7 +52,7 @@ while ($arg=shift) { elsif ($arg eq "--Q") { $queue = shift; } elsif ($arg eq "--T") { $queue_type = shift; } elsif ($arg eq "--R") { $restart_in = shift; } - else {$arg_pass .= " $arg "; } + else {$arg_pass .= " $arg " ; $arg_pass .= shift if (shift) } } ($in and $out) || print_usage(); debian/patches/series0000644000000000000000000000002612201651321012021 0ustar enable_help2man.patch debian/links0000644000000000000000000000235012203212144010220 0ustar 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-454 usr/bin/cdhit-454 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 debian/watch0000644000000000000000000000020311744730045010217 0ustar version=3 http://code.google.com/p/cdhit/downloads/list?can=1 \ .*/cd-hit-v([-.\d]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip) debian/changelog0000644000000000000000000000516612203227102011037 0ustar cd-hit (4.6.1-2012-08-27-2) unstable; urgency=low * Take over changes from BioLinux -- Andreas Tille Thu, 15 Aug 2013 21:36:49 +0200 cd-hit (4.6.1-2012-08-27-1biolinux1) precise; urgency=low * Rebuild for Precice * Add new cdhit-454 to /usr/bin, including help2man manpage * Remove dependency on openmpi, as cd-hit doesn't use it at all. (It uses the -fopenmp compiler flag; maybe there was some confusion?) -- Tim Booth Thu, 15 Aug 2013 17:00:41 +0100 cd-hit (4.6.1-2012-08-27-1) unstable; urgency=low * New upstream version (adapted patches) * debian/control: - cme fix dpkg-control - use anonscm in Vcs fields -- Andreas Tille Sun, 11 Aug 2013 10:51:30 +0200 cd-hit (4.6-2012-04-25-1) unstable; urgency=low * New upstream version incorporating the previous patches as well as the LaTeX source of the documentation * debian/patches/use-dpkg-buildflags.patch: Make sure hardening flags will really propagate * debian/{control,rules}: Use mpi version of cd-hit * README.Debian: Tell users that we are using mpi and they should ask for an alternative if needed * debian/*.1, debian/manpages: Deleted in favour of autogenerated manpages using help2man; Remark: the manually edited pages were slightly better regarding "SEE ALSO" and "AUTHORS" sections but it is better to auto-generate the pages to stay with changes of future versions * debian/rules: Use help2man 2 create manpages whereever possible * debian/patches/enable_help2man.patch: Fix some minor issues to get less error output in man pages -- Andreas Tille Thu, 26 Apr 2012 07:54:23 +0200 cd-hit (4.5.8-2012-03-24-1) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * New upstream version * debian/watch: Fixed to reflect the change on code.google.com * debian/control: Standards-Version: 3.9.3 (no changes needed) * debian/copyright: Fixed DEP5 and verified using cme fix dpkg-copyright * debian/patches/gcc-4.7.patch: Enable building with g++-4.7 Closes: #667134 * debian/upstream: - use BibTeX format to specify author - Move DOI+PMID to References - Differentiate between URl and eprint * debhelper 9 (control+compat) -- Andreas Tille Sun, 22 Apr 2012 18:06:41 +0200 cd-hit (4.5.7-1) unstable; urgency=low * Initial release (Closes: #652074) * This package is recommended by the package qiime and thus it also Closes: #651983 -- Andreas Tille Wed, 14 Dec 2011 14:39:32 +0100 debian/compat0000644000000000000000000000000211745026435010373 0ustar 9 debian/control0000644000000000000000000000224412203212144010562 0ustar Source: cd-hit Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), help2man Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cd-hit/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cd-hit/trunk/ Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ 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.