Merge branch 'hotfix/1.0.2'

Dockerfile

@@ -1,9 +1,9 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:1.0.6
+FROM  quay.io/wtsicgp/dockstore-cgpmap:1.0.7
 
 MAINTAINER  [email protected]
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="1.0.1" \
+      version="1.0.2" \
       description="The CGP WXS pipeline for dockstore.org"
 
 USER  root
@@ -13,11 +13,12 @@ ENV PATH $OPT/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
 
 ADD build/apt-build.sh build/
-ADD build/perllib-build.sh build/
-ADD build/opt-build.sh build/
-
 RUN bash build/apt-build.sh
+
+ADD build/perllib-build.sh build/
 RUN bash build/perllib-build.sh
+
+ADD build/opt-build.sh build/
 RUN bash build/opt-build.sh
 
 ADD scripts/analysisWXS.sh $OPT/bin/analysisWXS.sh

Dockstore.cwl

@@ -19,7 +19,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:1.0.1"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:1.0.2"
 
 hints:
   - class: ResourceRequirement
@@ -112,27 +112,12 @@ outputs:
   result_archive:
     type: File
     outputBinding:
-      glob: WXS_*_vs_*.tar.gz
+      glob: WXS_*_vs_*.result.tar.gz
 
   # named like this so can be converted to a secondaryFile set once supported by dockstore cli
-  time_cgpPindel:
+  timings:
     type: File
     outputBinding:
-      glob:  WXS_*_vs_*.time.cgpPindel
-
-  time_cgpPindel_annot:
-    type: File
-    outputBinding:
-      glob:  WXS_*_vs_*.time.cgpPindel_annot
-
-  time_CaVEMan:
-    type: File
-    outputBinding:
-      glob:  WXS_*_vs_*.time.CaVEMan
-
-  time_CaVEMan_annot:
-    type: File
-    outputBinding:
-      glob:  WXS_*_vs_*.time.CaVEMan_annot
+      glob:  WXS_*_vs_*.timings.tar.gz
 
 baseCommand: ["/opt/wtsi-cgp/bin/ds-wrapper.pl"]

build/opt-build.sh

@@ -1,54 +1,60 @@
 #!/bin/bash
 
-set -uxe
+set -xe
 
-mkdir -p /tmp/downloads
+if [[ -z "${TMPDIR}" ]]; then
+  TMPDIR=/tmp
+fi
 
-cd /tmp/downloads
+set -u
+
+mkdir -p $TMPDIR/downloads
+
+cd $TMPDIR/downloads
 
 # cgpVcf
 curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpVcf/archive/v2.1.1.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
+mkdir $TMPDIR/downloads/distro
+bsdtar -C $TMPDIR/downloads/distro --strip-components 1 -xf distro.zip
+cd $TMPDIR/downloads/distro
 ./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
+cd $TMPDIR/downloads
+rm -rf distro.zip $TMPDIR/downloads/distro /tmp/hts_cache
 
 # cgpPindel
 curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpPindel/archive/v2.1.0.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
+mkdir $TMPDIR/downloads/distro
+bsdtar -C $TMPDIR/downloads/distro --strip-components 1 -xf distro.zip
+cd $TMPDIR/downloads/distro
 ./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
+cd $TMPDIR/downloads
+rm -rf distro.zip $TMPDIR/downloads/distro /tmp/hts_cache
 
 # cgpCaVEManPostProcessing
 curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpCaVEManPostProcessing/archive/1.6.6.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
+mkdir $TMPDIR/downloads/distro
+bsdtar -C $TMPDIR/downloads/distro --strip-components 1 -xf distro.zip
+cd $TMPDIR/downloads/distro
 ./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
+cd $TMPDIR/downloads
+rm -rf distro.zip $TMPDIR/downloads/distro /tmp/hts_cache
 
 # cgpCaVEManWrapper
-curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpCaVEManWrapper/archive/1.10.1.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
+curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpCaVEManWrapper/archive/1.10.3.zip
+mkdir $TMPDIR/downloads/distro
+bsdtar -C $TMPDIR/downloads/distro --strip-components 1 -xf distro.zip
+cd $TMPDIR/downloads/distro
 ./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
+cd $TMPDIR/downloads
+rm -rf distro.zip $TMPDIR/downloads/distro /tmp/hts_cache
 
 # VAGrENT
-curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/VAGrENT/archive/v3.2.0.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
+curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/VAGrENT/archive/v3.2.1.zip
+mkdir $TMPDIR/downloads/distro
+bsdtar -C $TMPDIR/downloads/distro --strip-components 1 -xf distro.zip
+cd $TMPDIR/downloads/distro
 ./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
+cd $TMPDIR/downloads
+rm -rf distro.zip $TMPDIR/downloads/distro /tmp/hts_cache
 
-rm -rf /tmp/downloads
+rm -rf $TMPDIR/downloads

examples/analysis_config.local.json

@@ -24,20 +24,8 @@
     "path": "/tmp/result_WXS.tar.gz",
     "class": "File"
   },
-  "time_cgpPindel": {
-    "path": "/tmp/time.cgpPindel",
-    "class": "File"
-  },
-  "time_cgpPindel_annot": {
-    "path": "/tmp/time.cgpPindel_annot",
-    "class": "File"
-  },
-  "time_CaVEMan": {
-    "path": "/tmp/time.CaVEMan",
-    "class": "File"
-  },
-  "time_CaVEMan_annot": {
-    "path": "/tmp/time.CaVEMan_annot",
+  "timings": {
+    "path": "/tmp/timings_WXS.tar.gz",
     "class": "File"
   }
 }

scripts/analysisWXS.sh

@@ -16,7 +16,7 @@ run_parallel () {
       sleep 1 # gnu sleep allows floating point here...
     done
 
-    CMD="/usr/bin/time -f $TIME_FORMAT -o $OUTPUT_DIR/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.time.$key ${do_parallel[$key]}"
+    CMD="/usr/bin/time -f $TIME_FORMAT -o $OUTPUT_DIR/timings/${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.time.$key ${do_parallel[$key]}"
 
     echo -e "\tStarting $key"
     set -x
@@ -64,6 +64,7 @@ source $PARAM_FILE
 
 TMP=$OUTPUT_DIR/tmp
 mkdir -p $TMP
+mkdir -p $OUTPUT_DIR/timings
 
 if [ -z ${CPU+x} ]; then
   CPU=`grep -c ^processor /proc/cpuinfo`
@@ -211,7 +212,9 @@ run_parallel $CPU do_parallel
 rm -rf $OUTPUT_DIR/${NAME_MT}_vs_${NAME_WT}/*/logs
 
 echo 'Package results'
-tar -C $OUTPUT_DIR -zcf ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.tar.gz ${NAME_MT}_vs_${NAME_WT}
+# timings first
+tar -C $OUTPUT_DIR -zcf ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.timings.tar.gz timings
+tar -C $OUTPUT_DIR -zcf ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.result.tar.gz ${NAME_MT}_vs_${NAME_WT}
 cp $PARAM_FILE ${PROTOCOL}_${NAME_MT}_vs_${NAME_WT}.run.params
 
 # run any post-exec step

scripts/ds-wrapper.pl

@@ -80,6 +80,9 @@
 
 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
+printf $FH "PCAP_THREADED_NO_SCRIPT=1\n";
+printf $FH "PCAP_THREADED_FORCE_SYNC=1\n";
 # hard-coded
 printf $FH "PROTOCOL=WXS\n";
 # required options