diff --git a/Makefile.PL b/Makefile.PL index ad346ee..6ea20d1 100644 --- 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 index 693c01a..e883563 100755 --- 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 index 39837c4..d4c9938 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/PCAP.pm b/lib/PCAP.pm index 4101943..3948381 100644 --- 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 index 986dbce..f34deee 100755 --- 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