Upgraded biobambam, removed old bwa versions

ICGC-TCGA-PanCancer · Feb 5, 2015 · 8078ad6 · 8078ad6
1 parent d950978
commit 8078ad6
Show file tree

Hide file tree

Showing 6 changed files with 33 additions and 32 deletions.
diff --git 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
@@ -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
@@ -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
diff --git 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
@@ -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 = (