Merge branch 'hotfix/1.0.3'

cancerit · Mar 25, 2017 · 3ad6bfa · 3ad6bfa
2 parents f295524 + e2a4500
commit 3ad6bfa
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Showing 5 changed files with 14 additions and 8 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,8 @@
+### 1.0.3
+* Export the `PCAP_THREADED_*` variables
+* Fixed #8, #9, #10
+* Updated base image to pull in fix required for `PCAP_THREADED_LOADBACKOFF`
+
 ### 1.0.2
 * Update BRASS to handle data that is _very_ quiet
 * Fix up the wrapper timings file so it is captured properly

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,9 @@
-FROM  quay.io/wtsicgp/dockstore-cgpwxs:2.0.4
+FROM  quay.io/wtsicgp/dockstore-cgpwxs:2.0.5
 
 MAINTAINER  keiranmraine@gmail.com
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="1.0.2" \
+      version="1.0.3" \
       description="The CGP WGS pipeline for dockstore.org"
 
 USER  root

diff --git a/Dockstore.cwl b/Dockstore.cwl
@@ -19,7 +19,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:1.0.2"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:1.0.3"
 
 hints:
   - class: ResourceRequirement

diff --git a/scripts/analysisWGS.sh b/scripts/analysisWGS.sh
@@ -29,7 +29,7 @@ run_parallel () {
 
     if [ $BAD_JOBS -ne 0 ]; then
       DISPLAY_BAD=`grep -LF 'WRAPPER_EXIT: 0' $OUTPUT_DIR/*.wrapper.log`
-      >&2 echo -e "ERRORS OCCURED:\n$DISPLAY_BAD"
+      >&2 echo -e "ERRORS OCCURRED:\n$DISPLAY_BAD"
       exit 1
     fi
 
@@ -61,6 +61,7 @@ if [ ! -f $PARAM_FILE ]; then
   exit 1
 fi
 source $PARAM_FILE
+env
 
 TMP=$OUTPUT_DIR/tmp
 mkdir -p $TMP

diff --git a/scripts/ds-wrapper.pl b/scripts/ds-wrapper.pl
@@ -79,7 +79,7 @@
 ref_unpack($ref_area, $opts{'a'});
 ref_unpack($ref_area, $opts{'si'});
 ref_unpack($ref_area, $opts{'cs'});
-ref_unpack($ref_area, $opts{'sc'});
+ref_unpack($ref_area, $opts{'sc'}) if(exists $opts{'sb'});
 
 ## now complete the caveman flaging file correctly
 my $ini = add_species_flag_ini($opts{'sp'}, "$ref_area/caveman/flag.vcf.config.WGS.ini");
@@ -90,9 +90,9 @@
 my $run_file = $ENV{HOME}.'/run.params';
 open my $FH,'>',$run_file or die "Failed to write to $run_file: $!";
 # Force explicit checking of file flush
-print $FH "PCAP_THREADED_NO_SCRIPT=1\n";
-print $FH "PCAP_THREADED_FORCE_SYNC=1\n";
-#print $FH "PCAP_THREADED_LOADBACKOFF=1\n";
+print $FH "export PCAP_THREADED_NO_SCRIPT=1\n";
+print $FH "export PCAP_THREADED_FORCE_SYNC=1\n";
+print $FH "export PCAP_THREADED_LOADBACKOFF=1\n";
 # hard-coded
 printf $FH "PROTOCOL=WGS\n";
 # required options