debian/0000755000000000000000000000000012144460040007161 5ustar debian/rules0000755000000000000000000000003612144460040010240 0ustar #!/usr/bin/make -f %: dh $@ debian/control0000644000000000000000000000265512144460040010574 0ustar Source: libgenome-model-tools-music-perl Maintainer: Debian Perl Group Uploaders: Olivier Sallou , Debian Med Packaging Team Section: perl Priority: optional Build-Depends: debhelper (>= 9), libmodule-build-perl (>= 0.390000) | perl (>= 5.15.2) Build-Depends-Indep: perl, libgenome-perl, libregexp-common-perl, libstatistics-distributions-perl, libtext-csv-xs-perl, libbit-vector-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libgenome-model-tools-music-perl.git Vcs-Git: git://anonscm.debian.org/pkg-perl/packages/libgenome-model-tools-music-perl.git Homepage: https://metacpan.org/release/Genome-Model-Tools-Music/ Package: libgenome-model-tools-music-perl Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libgenome-perl, libregexp-common-perl, libstatistics-distributions-perl, libtext-csv-xs-perl, libbit-vector-perl Description: module for finding mutations of significance in cancer The MuSiC suite is a set of tools aimed at discovering the significance of somatic mutations found within a given cohort of cancer samples, and with respect to a variety of external data sources. debian/README.source0000644000000000000000000000047212144460040011343 0ustar Lintian warnings on manpage-has-bad-whatis have been overriden because pod files are not generated the usual way. Pod files are generated with UR::Namespace::Command::Update::Doc->execute in Build.PL. Current code of UR command misses what-is usual additional info. This does not impact global man pages layout. debian/source/0000755000000000000000000000000012144460040010461 5ustar debian/source/format0000644000000000000000000000001412144460040011667 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000026212144460040011033 0ustar libgenome-model-tools-music-perl (0.04-1) unstable; urgency=low * Initial Release (Closes: #701470). -- Olivier Sallou Sat, 23 Feb 2013 15:39:49 +0100 debian/compat0000644000000000000000000000000212144460040010357 0ustar 9 debian/libgenome-model-tools-music-perl.lintian-overrides0000644000000000000000000000011712144460040021013 0ustar libgenome-model-tools-music-perl: manpage-has-bad-whatis-entry usr/share/man/* debian/patches/0000755000000000000000000000000012144460040010610 5ustar debian/patches/series0000644000000000000000000000001612144460040012022 0ustar 01-fixpod2man debian/patches/01-fixpod2man0000644000000000000000000000313312144460040013020 0ustar Subject: Fix pod2man errors Description: upstream contains pod errors Author: Olivier Sallou Last-Updated: 2013-05-01 Forwarded: yes Bug: https://rt.cpan.org/Public/Bug/Display.html?id=84967 --- a/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm +++ b/lib/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm @@ -60,7 +60,6 @@ up these base-counts across all ROIs of each gene in the sample, but covered bases that lie within overlapping ROIs are not counted more than once towards these total counts. -=back HELP } @@ -110,6 +109,8 @@ =back +=back + EOS ); } --- a/lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm +++ b/lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm @@ -135,7 +135,7 @@ =item * Columns must be ordered as such: -=item [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ] +=item * [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ] =item * The 'analysis_type' column must contain either "Q", indicating a quantative trait, or "B", indicating a binary trait will be examined. --- a/lib/Genome/Model/Tools/Music/PathScan.pm +++ b/lib/Genome/Model/Tools/Music/PathScan.pm @@ -116,6 +116,7 @@ =back =back + EOS ); } --- a/lib/Genome/Model/Tools/Music/Smg.pm +++ b/lib/Genome/Model/Tools/Music/Smg.pm @@ -83,6 +83,7 @@ =back =back + EOS ); } --- a/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm +++ b/lib/Genome/Model/Tools/Music/Bmr/CalcCovg.pm @@ -83,6 +83,7 @@ cmd-list-file and cmd-prefix arguments or you will just be re-creating a list of commands. =back + HELP } debian/copyright0000644000000000000000000000442712144460040011123 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-Model-Tools-Music/ Files: * Copyright: 2007-2011 Washington University in St. Louis License: LGPL-3 Comment: README says "same terms as Perl itself"; we are assuming that this is boilerplate text from the build tools, since the code has explicit statements about the LGPL-3. A bug has been created upstream to clarify the situation but upstream bug system does not seem to be followed anymore since 2012. Bug ref: https://rt.cpan.org/Public/Bug/Display.html?id=85079 Files: lib/Genome/Model/Tools/Music/PathScan/* Copyright: 2009 Washington University in St. Louis License: GPL-2+ 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: 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, or (at your option) any later version. . On Debian systems, the complete text of version 2 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. 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/watch0000644000000000000000000000021612144460040010211 0ustar version=3 https://metacpan.org/release/Genome-Model-Tools-Music/ .*/Genome-Model-Tools-Music-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$