Merge branch 'release/1.0.0'

Author: keiranmraine

CHANGES.md

@@ -0,0 +1,5 @@
+### 1.0.0
+* Test data in `examples/analysis_config.local.json` moved to a non-expiring location.
+* See [dockstore-cgpwxs:2.0.0](https://github.com/cancerit/dockstore-cgpwxs/releases/tag/2.0.0)
+* Significant shrinking of image.
+* Re-org of exec order to reduce overall runtime.

Dockerfile

@@ -1,32 +1,36 @@
-FROM  quay.io/wtsicgp/dockstore-cgpwxs:1.0.4
+FROM  quay.io/wtsicgp/dockstore-cgpwxs:2.0.1
 
 MAINTAINER  keiranmraine@gmail.com
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="0.1.1" \
+      version="1.0.0" \
       description="The CGP WGS pipeline for dockstore.org"
 
 USER  root
 
 ENV OPT /opt/wtsi-cgp
 ENV PATH $OPT/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
 ENV R_LIBS $OPT/R-lib
 ENV R_LIBS_USER $R_LIBS
 
 COPY build/apt-build.sh build/
 RUN bash build/apt-build.sh
 
+COPY build/r-build.sh build/
+COPY build/rlib-build.R build/
+RUN bash build/r-build.sh $OPT 1
+
 COPY build/perllib-build.sh build/
 RUN bash build/perllib-build.sh
 
 COPY build/opt-build.sh build/
-RUN bash build/opt-build.sh
+RUN bash build/opt-build.sh $OPT
 
 COPY scripts/analysisWGS.sh $OPT/bin/analysisWGS.sh
 COPY scripts/ds-wrapper.pl $OPT/bin/ds-wrapper.pl
-COPY bin/ssearch36-fasta-36.3.8d-linux64 $OPT/bin/ssearch36
-RUN chmod a+x $OPT/bin/analysisWGS.sh $OPT/bin/ds-wrapper.pl $OPT/bin/ssearch36
+RUN chmod a+x $OPT/bin/analysisWGS.sh $OPT/bin/ds-wrapper.pl
 
 USER    ubuntu
 WORKDIR /home/ubuntu

Dockstore.cwl

@@ -19,11 +19,11 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:0.1.1"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwgs:1.0.0"
 
 hints:
   - class: ResourceRequirement
-    coresMin: 1 # works but long, 8 recommended
+    coresMin: 1 # works but long, 24 recommended
     ramMin: 32000
     outdirMin: 20000
 
@@ -119,6 +119,14 @@ inputs:
       separate: true
       shellQuote: true
 
+  skipbb:
+    type: boolean?
+    doc: "Skip Battenberg allele counts"
+    inputBinding:
+      prefix: -skipbb
+      position: 11
+      separate: true
+
 outputs:
   run_params:
     type: File

bin/ssearch36-fasta-36.3.8d-linux64

@@ -2,12 +2,10 @@
 
 set -eux
 
-apt-get -yq update
-apt-get -yq install gfortran
-apt-get -yq install r-base r-base-dev
-
-### security upgrades and cleanup
-apt-get -yq install unattended-upgrades
-unattended-upgrades
-apt -yq autoremove
-apt-get clean
+apt-get update
+apt-get install -qy --no-install-recommends libreadline6-dev
+apt-get install -qy --no-install-recommends libcairo2-dev
+apt-get install -qy --no-install-recommends gfortran
+apt-get install -qy --no-install-recommends unzip
+apt-get install -qy --no-install-recommends libboost-all-dev
+apt-get install -qy --no-install-recommends libpstreams-dev