debian/0000755000000000000000000000000012214540433007164 5ustar debian/gbp.conf0000644000000000000000000000023612214540365010610 0ustar [DEFAULT] pristine-tar = True [git-buildpackage] # use this for more svn-buildpackage like behaviour: export-dir = ../build-area/ tarball-dir = ../tarballs/ debian/control0000644000000000000000000000322712214540365010577 0ustar Source: grinder Maintainer: Debian Med Packaging Team Uploaders: Florent Angly , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Build-Depends-Indep: libbio-perl-perl, libgetopt-euclid-perl (>= 0.2.8), libmath-random-mt-perl (>= 1.13), help2man Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/grinder.git Vcs-Git: git://anonscm.debian.org/debian-med/grinder.git Homepage: http://sourceforge.net/projects/biogrinder/ Package: grinder Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl, libgetopt-euclid-perl (>= 0.2.8), libmath-random-mt-perl (>= 1.13) Description: Versatile omics shotgun and amplicon sequencing read simulator Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. . Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced. debian/rules0000755000000000000000000000627212214540365010257 0ustar #!/usr/bin/make -f PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') AUTHOR := Florent Angly VERSION := $(shell LC_ALL=C dpkg-parsechangelog | awk '/^Version:/{print $$2;}' | sed -e 's,-[^-]*$$,,g') SECTION := 1 MANDIR := debian/man NAME1 = $(PACKAGE) SCRIPT1 = script/$(NAME1) DESC1 = 'Versatile omics shotgun and amplicon sequencing read simulator' MAN1 = $(MANDIR)/$(NAME1).$(SECTION) NAME2 = average_genome_size SCRIPT2 = utils/$(NAME2) DESC2 = 'Calculate the average genome size in Grinder libraries' MAN2 = $(MANDIR)/$(NAME2).$(SECTION) NAME3 = change_paired_read_orientation SCRIPT3 = utils/$(NAME3) DESC3 = 'Reverses the orientation of each paired\-end FASTA sequence' MAN3 = $(MANDIR)/$(NAME3).$(SECTION) define MORE [see also] .BR grinder (7), .BR $(NAME1) ($(SECTION)), .BR $(NAME2) ($(SECTION)) and .BR $(NAME3) ($(SECTION)). endef export MORE MOREFILE = $(MANDIR)/more.$(SECTION) %: dh $@ override_dh_auto_configure: # It seems libbio-perl-perl is integrating actively code # from grinder and includes it into their distribution. Finally # now are all modules from the Bio directory integrated into # BioPerl. The single file moving was kept just for the reason # to have some template once a new Grinder version might come up # with new code mkdir -p _disposal/Bio # MYMETA.yml will be changed and not reverted in clean target - use the chance to conserve it here cp -a MYMETA.yml _disposal mv lib/Bio/PrimarySeq*.pm _disposal/Bio mkdir -p _disposal/Bio/DB mv lib/Bio/DB/Fasta.pm _disposal/Bio/DB mv lib/Bio/DB/IndexedBase.pm _disposal/Bio/DB mkdir -p _disposal/Bio/Seq mv lib/Bio/Seq/SeqFastaSpeedFactory.pm _disposal/Bio/Seq mv lib/Bio/Seq/SimulatedRead.pm _disposal/Bio/Seq mkdir -p _disposal/Bio/SeqFeature mv lib/Bio/SeqFeature/Amplicon.pm _disposal/Bio/SeqFeature mv lib/Bio/SeqFeature/Primer.pm _disposal/Bio/SeqFeature mv lib/Bio/SeqFeature/SubSeq.pm _disposal/Bio/SeqFeature mkdir -p _disposal/Bio/Tools mv lib/Bio/Tools/AmpliconSearch.pm _disposal/Bio/Tools mv lib/Bio/Tools/IUPAC.pm _disposal/Bio/Tools dh_auto_configure # Because of Grinder's random output, some tests are brittle and may fail... # Only test that the program loads successfully override_dh_auto_test: $(MAKE) testdb TEST_FILE=t/00-load.t TESTDB_SW='' # Generate manpages on the fly override_dh_auto_build: mkdir -p $(MANDIR) echo "$$MORE" > $(MOREFILE) help2man --no-discard-stderr --name $(DESC1) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN1) $(SCRIPT1) help2man --no-discard-stderr --name $(DESC2) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN2) $(SCRIPT2) help2man --no-discard-stderr --name $(DESC3) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN3) $(SCRIPT3) rm $(MOREFILE) dh_auto_build override_dh_auto_clean: dh_auto_clean rm -rf $(MANDIR) if [ -d _disposal ] ; then \ if [ -e _disposal/MYMETA.yml ] ; then mv _disposal/MYMETA.yml . ; fi ; \ for pm in `cd _disposal ; find Bio -type f ; cd ..` ; do \ mv _disposal/$${pm} lib/$${pm} ; \ done ; \ fi rm -rf _disposal debian/watch0000644000000000000000000000013212214540365010215 0ustar version=3 http://sf.net/biogrinder/Grinder-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/upstream0000644000000000000000000000073512214540365010760 0ustar Reference: Author: Florent E. Angly and Dana Willner and Forest Rohwer and Philip Hugenholtz and Gene W. Tyson Title: "Grinder: a versatile amplicon and shotgun sequence simulator" Journal: Nucleic Acids Research Year: 2012 Volume: Epub ahead of print DOI: 10.1093/nar/gks251 PMID: 22434876 URL: http://nar.oxfordjournals.org/content/early/2012/03/19/nar.gks251.abstract eprint: http://nar.oxfordjournals.org/content/early/2012/03/19/nar.gks251.full.pdf+html debian/copyright0000644000000000000000000000417012214540365011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Grinder Upstream-Contact: Florent Angly Source: http://sourceforge.net/projects/biogrinder/files/ Files: * Copyright: 2009-2011, Florent Angly License: GPL-3+ Files: debian/* Copyright: 2012, Florent Angly License: GPL-3+ Files: inc/Module/* Copyright: 2002-2011, Adam Kennedy 2002-2011, Audrey Tang 2002-2011, Brian Ingerson License: Artistic or GPL-1+ Files: inc/Module/Install/AuthorRequires.pm Copyright: 2009, Florian Ragwitz License: Artistic or GPL-1+ Files: inc/Module/Install/AutoLicense.pm Copyright: 2010, Chris Williams License: Artistic or GPL-1+ Files: inc/Module/Install/AutoManifest.pm Copyright: 2008, Hans Dieter Pearcey License: Artistic or GPL-1+ Files: inc/Module/Install/ReadmeFromPod.pm Copyright: 2010, Chris Williams License: Artistic or GPL-1+ License: Artistic This program is free software; you can redistribute it and/or modify it under the terms of the Artistic License, which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in `/usr/share/common-licenses/Artistic'. License: GPL-1+ 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 1, or (at your option) any later version. . On Debian systems, the complete text of version 1 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-1'. License: GPL-3+ 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; version 3 dated June, 2007, or (at your option) any later version. . On Debian systems, the complete text of version 3 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-3'. debian/source/0000755000000000000000000000000012214540365010470 5ustar debian/source/format0000644000000000000000000000001412214540365011676 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000342012214540365011041 0ustar grinder (0.5.3-3) unstable; urgency=low * debian/rules: - Move more duplicates from libbio-perl-perl out of the way Closes: #722650 Remark: It seems libbio-perl-perl is integrating actively code from grinder and includes it into their distribution. Finally now are all modules from the Bio directory integrated into BioPerl. - Obtain version from changelog instead of setting it manually (which is in danger to age without noticing) * debian/control: anonscm in Vcs fields -- Andreas Tille Fri, 13 Sep 2013 08:25:06 +0200 grinder (0.5.3-2) unstable; urgency=low * debian/rules: - clean target should recreate original tarball - Move some files duplicated from bioperl out of the way in configure step and restore them in clean target Closes: #718407 -- Andreas Tille Thu, 01 Aug 2013 11:05:04 +0200 grinder (0.5.3-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - debhelper 9 -- Andreas Tille Tue, 30 Jul 2013 12:54:05 +0200 grinder (0.4.5-1) unstable; urgency=low * New upstream version * debian/upstream: Added citations * debian/control: Standards-Version: 3.9.3 (no changes needed) * debian/copyright: Use `cme fix dpkg-copyright` to fix Format URL -- Andreas Tille Thu, 03 May 2012 08:30:08 +0200 grinder (0.4.4-2) unstable; urgency=low * Team upload. [ Florent Angly ] * Added copyright information for files in inc/. -- Charles Plessy Sun, 29 Jan 2012 15:15:08 +0900 grinder (0.4.4-1) REJECTED; urgency=low * Initial Release. Closes: #654394 -- Florent Angly Fri, 20 Jan 2012 11:41:11 +1000 debian/compat0000644000000000000000000000000212214540365010366 0ustar 9 debian/grinder.manpages0000644000000000000000000000001712214540365012335 0ustar debian/man/*.1 debian/grinder.docs0000644000000000000000000000002212214540365011466 0ustar README.htm README