Merge branch 'hotfix/v1.11.1'

ICGC-TCGA-PanCancer · Jan 29, 2016 · 536af6c · 536af6c
2 parents 8fa4aa0 + 53a3270
commit 536af6c
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Showing 5 changed files with 11 additions and 5 deletions.
diff --git a/Makefile.PL b/Makefile.PL
@@ -62,6 +62,8 @@ WriteMakefile(
                      'Sub::Exporter::Progressive' => 0.001011,
                      'XML::Simple' => 2.20,
                      'version' => 0.9912,
+                     'JSON' => 2.90,
+                     'JSON::XS' => 3.01,
                    }
 );
 

diff --git a/bin/gnos_pull.pl b/bin/gnos_pull.pl
@@ -47,7 +47,7 @@
 use PCAP::Cli;
 
 const my @ANALYSIS_TYPES => (qw(ALIGNMENTS CALLS));
-const my @AVAILABLE_COMPOSITE_FILTERS => (qw(caller max_dataset_GB multi_tumour sanger_version broad_version dkfz_embl_version jamboree_approved manual_donor_blacklist));
+const my @AVAILABLE_COMPOSITE_FILTERS => (qw(not_sanger_workflow caller max_dataset_GB multi_tumour sanger_version broad_version dkfz_embl_version jamboree_approved manual_donor_blacklist));
 const my $DEFAULT_URL => 'http://pancancer.info/gnos_metadata/latest';
 const my $GTDL_COMMAND => '%s%s --max-children 3 --rate-limit 200 -vv -c %s -d %scghub/data/analysis/download/%s -p %s';
 
@@ -382,6 +382,11 @@ sub pull_calls {
 
     next if(exists $options->{'COMPOSITE_FILTERS'}->{$caller.'_version'} && $options->{'COMPOSITE_FILTERS'}->{$caller.'_version'} ne $donor->{'variant_calling_results'}->{$caller.'_variant_calling'}->{'workflow_details'}->{'variant_workflow_version'});
 
+    if(exists $options->{'COMPOSITE_FILTERS'}->{not_sanger_workflow} && $options->{'COMPOSITE_FILTERS'}->{not_sanger_workflow} eq $donor->{'variant_calling_results'}->{'sanger_variant_calling'}->{'workflow_details'}->{'variant_workflow_name'}) {
+      warn "Skipping version $donor->{donor_unique_id} as version == $options->{COMPOSITE_FILTERS}->{not_sanger_workflow}\n" if($options->{debug});
+      next;
+    }
+
     # if we can get access to transfer metrics we want to select the fastest, or use list in config file
     my $repo = select_repo($options, $donor->{'variant_calling_results'}->{$caller.'_variant_calling'}->{'gnos_repo'});
     unless(exists $options->{'keys'}->{$repo}) {

diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.11.0';
+our $VERSION = '1.11.1';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -73,6 +73,7 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,bwa,samtools',
                             '1.9.4'  => 'biobambam',
                             '1.10.0'  => 'biobambam',
                             '1.11.0'  => 'biobambam',
+                            '1.11.1'  => 'biobambam',
                           );
 
 sub license {

diff --git a/setup.sh b/setup.sh
@@ -68,8 +68,7 @@ cd $INIT_DIR
 unset PERL5LIB
 ARCHNAME=`perl -e 'use Config; print $Config{archname};'`
 PERLROOT=$INST_PATH/lib/perl5
-PERLARCH=$PERLROOT/$ARCHNAME
-export PERL5LIB="$PERLROOT:$PERLARCH"
+export PERL5LIB="$PERLROOT"
 
 #create a location to build dependencies
 SETUP_DIR=$INIT_DIR/install_tmp
@@ -287,7 +286,6 @@ echo "Please add the following to beginning of path:"
 echo "  $INST_PATH/bin"
 echo "Please add the following to beginning of PERL5LIB:"
 echo "  $PERLROOT"
-echo "  $PERLARCH"
 echo
 
 exit 0