debian/0000755000000000000000000000000012132564573007176 5ustar debian/rules0000755000000000000000000000060612132564573010260 0ustar #!/usr/bin/make -f PACKAGE = $(shell dh_listpackages) TMP = $(CURDIR)/debian/$(PACKAGE) %: dh $@ override_dh_clean: rm -rf cmd-bindoc dh_clean override_dh_auto_build: dh_auto_build pod2man bin/genome > cmd-bindoc/genome.1 pod2man bin/gmt > cmd-bindoc/gmt.1 override_dh_installman: dh_installman # Remove empty files $(RM) -v $(TMP)/usr/share/man/man1/genome-model-tools* debian/control0000644000000000000000000000257312132564573010610 0ustar Source: libgenome-perl Maintainer: Debian Perl Group Uploaders: Olivier Sallou , Debian Med Packaging Team Section: perl Priority: optional Build-Depends: debhelper (>= 8) Build-Depends-Indep: libgetopt-complete-perl, libio-string-perl, libur-perl, perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libgenome-perl.git Vcs-Git: git://git.debian.org/pkg-perl/packages/libgenome-perl.git Homepage: https://metacpan.org/release/Genome/ Package: libgenome-perl Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libgetopt-complete-perl, libio-string-perl, libur-perl Description: pipelines, tools, and data management for genomics This is the base namespace module for the Genome software tree. . That tree has several primary components: . Genome::Model: a data modeling pipeline management system for genomics . Genome::Model::Tools a tree of >1000 tools and tool wrappers for genomics . Genome::* a variety of sample tracking classes with an RDBMS back-end . Only the tools system is currently released. . See genome for a complete inventory of all tool packages, and for command-line access to those tools. debian/source/0000755000000000000000000000000012132564573010476 5ustar debian/source/format0000644000000000000000000000001412132564573011704 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000024012132564573011044 0ustar libgenome-perl (0.06-1) unstable; urgency=low * Initial Release (Closes: #701467). -- Olivier Sallou Sat, 23 Feb 2013 12:12:22 +0100 debian/libgenome-perl.manpages0000644000000000000000000000004512132564573013613 0ustar cmd-bindoc/genome.1 cmd-bindoc/gmt.1 debian/compat0000644000000000000000000000000212132564573010374 0ustar 8 debian/patches/0000755000000000000000000000000012132564573010625 5ustar debian/patches/spelling.patch0000644000000000000000000000125712132564573013470 0ustar Description: fix a spelling mistake Origin: vendor Bug: https://rt.cpan.org/Ticket/Display.html?id=84631 Forwarded: https://rt.cpan.org/Ticket/Display.html?id=84631 Author: gregor herrmann Last-Update: 2013-04-14 --- a/META.yml +++ b/META.yml @@ -1,5 +1,5 @@ --- -abstract: 'pipelines, tools, and data managment for genomics' +abstract: 'pipelines, tools, and data management for genomics' author: [] configure_requires: Module::Build: 0.36 --- a/lib/Genome.pm +++ b/lib/Genome.pm @@ -107,7 +107,7 @@ =head1 NAME -Genome - pipelines, tools, and data managment for genomics +Genome - pipelines, tools, and data management for genomics =head1 SYNOPSIS debian/patches/fix_man_whatis0000644000000000000000000000245112132564573013552 0ustar Subject: pod errors Description: some files contain wrong what-is section in pod. Author: Olivier Sallou Last-Updated: 2013-04-18 Forwarded: yes Bug: https://rt.cpan.org/Public/Bug/Display.html?id=84604 --- a/lib/Genome/Env/GENOME_DB.pm +++ b/lib/Genome/Env/GENOME_DB.pm @@ -2,7 +2,7 @@ =head1 NAME -GENOME_DB +GENOME_DB - Database root directory =head1 DESCRIPTION --- a/lib/Genome/Env/GENOME_SW.pm +++ b/lib/Genome/Env/GENOME_SW.pm @@ -2,7 +2,7 @@ =head1 NAME -GENOME_SW +GENOME_SW - Database root directory =head1 DESCRIPTION --- a/lib/Genome/Env/GENOME_SYS_NO_CLEANUP.pm +++ b/lib/Genome/Env/GENOME_SYS_NO_CLEANUP.pm @@ -2,7 +2,7 @@ =head1 NAME -GENOME_TEST_DEV +GENOME_TEST_DEV - Temp files cleanup condition =head1 DESCRIPTION --- a/lib/Genome/Env/GENOME_TEST_DEV.pm +++ b/lib/Genome/Env/GENOME_TEST_DEV.pm @@ -2,7 +2,7 @@ =head1 NAME -GENOME_TEST_DEV +GENOME_TEST_DEV - Code test condition =head1 DESCRIPTION --- a/lib/Genome/Sys.pm +++ b/lib/Genome/Sys.pm @@ -393,7 +393,7 @@ =head1 NAME -Genome::Sys +Genome::Sys - System layer =head1 VERSION --- a/lib/Genome/Vocabulary.pm +++ b/lib/Genome/Vocabulary.pm @@ -14,7 +14,7 @@ =head1 NAME -Genome::Vocabulary +Genome::Vocabulary - Domain specific terminology =head1 DESCRIPTION debian/patches/series0000644000000000000000000000003612132564573012041 0ustar fix_man_whatis spelling.patch debian/copyright0000644000000000000000000000263212132564573011134 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Genome Upstream-Contact: genome-dev@genome.wustl.edu Source: https://metacpan.org/release/Genome/ Files: * Copyright: 2007-2011 Washington University in St. Louis License: LGPL-3 Files: debian/* Copyright: 2013, Olivier Sallou 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: LGPL-3 This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser 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 Lesser General Public License can be found in `/usr/share/common-licenses/LGPL-3'. debian/watch0000644000000000000000000000015212132564573010225 0ustar version=3 https://metacpan.org/release/Genome/ .*/Genome-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$