diff --git a/MYMETA.json b/MYMETA.json index 49771ac..1d4e404 100644 --- a/MYMETA.json +++ b/MYMETA.json @@ -4,7 +4,7 @@ "unknown" ], "dynamic_config" : 0, - "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690", + "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560", "license" : [ "gpl_2" ], diff --git a/MYMETA.yml b/MYMETA.yml index 3614935..f093bde 100644 --- a/MYMETA.yml +++ b/MYMETA.yml @@ -3,38 +3,38 @@ abstract: unknown author: - unknown build_requires: - ExtUtils::MakeMaker: '0' + ExtUtils::MakeMaker: 0 configure_requires: - ExtUtils::MakeMaker: '0' + ExtUtils::MakeMaker: 0 dynamic_config: 0 -generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690' +generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560' license: gpl meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html - version: '1.4' + version: 1.4 name: PCAP no_index: directory: - t - inc requires: - Bio::DB::Sam: '1.39' - Bio::Root::Version: '1.006923' - Capture::Tiny: '0.24' - Const::Fast: '0.014' - Data::UUID: '1.219' - Devel::Cover: '1.09' - File::Which: '0.05' - GD: '2.52' - IPC::System::Simple: '1.25' - List::Util: '1.38' - Math::Gradient: '0.04' - Module::Build: '0.42' - Pod::Coverage: '0.23' - Proc::ProcessTable: '0.5' - Sub::Exporter::Progressive: '0.001011' - Term::UI: '0.42' - Test::Fatal: '0.013' - Try::Tiny: '0.19' - XML::Simple: '2.2' + Bio::DB::Sam: 1.39 + Bio::Root::Version: 1.006923 + Capture::Tiny: 0.24 + Const::Fast: 0.014 + Data::UUID: 1.219 + Devel::Cover: 1.09 + File::Which: 0.05 + GD: 2.52 + IPC::System::Simple: 1.25 + List::Util: 1.38 + Math::Gradient: 0.04 + Module::Build: 0.42 + Pod::Coverage: 0.23 + Proc::ProcessTable: 0.5 + Sub::Exporter::Progressive: 0.001011 + Term::UI: 0.42 + Test::Fatal: 0.013 + Try::Tiny: 0.19 + XML::Simple: 2.2 version: v1.2.3 diff --git a/bin/build_biobambam_relocatable.sh b/bin/build_biobambam_relocatable.sh index 52afe87..67343a5 100755 --- a/bin/build_biobambam_relocatable.sh +++ b/bin/build_biobambam_relocatable.sh @@ -1,8 +1,8 @@ #! /bin/bash -LIBMAUSVERSION=0.0.167-release-20140917101853 -BIOBAMBAMVERSION=0.0.171-release-20140917102804 +LIBMAUSVERSION=0.0.191-release-20150129231009 +BIOBAMBAMVERSION=0.0.185-release-20150116094537 SNAPPYVERSION=1.1.2 -IOLIBVERSION=1.13.7 +IOLIBVERSION=1.13.9 CHRPATHVERSION=0.16 BUILDDIR=${PWD} INSTALLDIR=${BUILDDIR}/install-dir diff --git a/docs.tar.gz b/docs.tar.gz index 6ed0cbf..0adfc78 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/PCAP.pm b/lib/PCAP.pm index de96124..3e06845 100644 --- a/lib/PCAP.pm +++ b/lib/PCAP.pm @@ -49,9 +49,10 @@ const my %UPGRADE_PATH => ( '0.1.0' => 'biobambam,bwa,samtools', '1.1.0' => 'biobambam,bwa,samtools', '1.1.1' => 'biobambam,bwa,samtools', '1.1.2' => 'biobambam,bwa,samtools', - '1.2.0' => '', # if later versions have new versions then all preceding need that tool listing - '1.2.1' => '', - '1.2.2' => '', + '1.2.0' => 'biobambam', # if later versions have new versions then all preceding need that tool listing + '1.2.1' => 'biobambam', + '1.2.2' => 'biobambam', + '1.3.0' => '', ); sub license { diff --git a/t/3_external_progs.t b/t/3_external_progs.t index 339d616..7c22922 100644 --- a/t/3_external_progs.t +++ b/t/3_external_progs.t @@ -12,8 +12,8 @@ use Capture::Tiny qw(capture); use Data::Dumper; const my @REQUIRED_PROGRAMS => qw(bamcollate2 bammarkduplicates bamsort bwa); -const my $BIOBAMBAM_VERSION => ['0.0.171']; -const my $BWA_VERSIONS => ['0.6.2','0.7.8','0.7.10']; +const my $BIOBAMBAM_VERSION => ['0.0.185']; +const my $BWA_VERSIONS => ['0.7.10']; # can't put regex in const my %EXPECTED_VERSION = (