Merge branch 'release/3.0.0'

.dockerignore

@@ -0,0 +1,5 @@
+/examples/
+/cwls/
+/git-hooks/
+/*.*
+/LICENSE

.travis.yml

@@ -4,11 +4,38 @@ notifications:
 
 sudo: false
 
+language: ruby
+
 services:
   - docker
 
 install:
- - docker build -t dockstore-cgpwxs .
+ - virtualenv -p python3 venv
+ - source venv/bin/activate
+ - pip install html5lib cwltool
 
 script:
+ # Validate CWL file(s)
+ - cwltool --validate cwls/cgpwxs.cwl
+ # Build and check docker image
+ - docker build -t dockstore-cgpwxs .
  - docker images | grep -c dockstore-cgpwxs
+ # Verify program from each inherited package is found (dockstore-cgpbigwig)
+ - docker run -t --rm dockstore-cgpwxs bwjoin --version
+ # Verify program from each inherited package is found (dockstore-cgpmap)
+ - docker run -t --rm dockstore-cgpwxs ds-cgpmap.pl -h
+ - docker run -t --rm dockstore-cgpwxs bwa_mem.pl -version
+ - docker run -t --rm dockstore-cgpwxs bammarkduplicates2 --version
+ - docker run -t --rm dockstore-cgpwxs samtools --version
+ - docker run -t --rm dockstore-cgpwxs bash -c 'bwa 2>&1 | grep Version'
+ # Verify a program from each new package is found (dockstore-cgpwxs)
+ - docker run -t --rm dockstore-cgpwxs ds-cgpwxs.pl -h
+ - docker run -t --rm dockstore-cgpwxs cgpVCFSplit.pl -version
+ - docker run -t --rm dockstore-cgpwxs vcftools --version
+ - docker run -t --rm dockstore-cgpwxs bedtools --version
+ - docker run -t --rm dockstore-cgpwxs bash -c 'pindel 2>&1 | grep Welcome'
+ - docker run -t --rm dockstore-cgpwxs pindel.pl -version
+ - docker run -t --rm dockstore-cgpwxs caveman --version
+ - docker run -t --rm dockstore-cgpwxs caveman.pl -version
+ - docker run -t --rm dockstore-cgpwxs cgpFlagCaVEMan.pl -version
+ - docker run -t --rm dockstore-cgpwxs AnnotateVcf.pl -version

CHANGES.md

@@ -1,47 +1,73 @@
-### 2.1.0
+# CHANGES
+
+## 3.0.0
+
+* See dockstore-cgpmap v3.0.0 (primarily adds mismatchQc)
+* CaVEMan and cgpPindel updated to use fragment based counting.
+  * You will need to update the reference pack to include the new flagging rules, see example `json`
+  files
+* VAGrENT update to v3.3.0, only affects generation of annotation cache not use of existing ones.
+* Using build stages to shrink images.
+* remove legacy PRE/POST-EXEC from cgpbox days, use dockstore if you want file provisioning.
+
+## 2.1.0
+
 * Fixes various sort order issues in CaVEMan, cgpPindel and VAGrENT affecting
 comparison of results from same inputs.
 
-### 2.0.7
+## 2.0.7
+
 * Bumps cgpPindel to [v2.2.3](https://github.com/cancerit/cgpPindel/releases/tag/v2.2.3) to fix bug in DI event collation.
 
-### 2.0.6
+## 2.0.6
+
 * Update base image to dockstore-cgpmap:2.0.3 (new PCAP-core for load management)
 * Bump cgpCaVEManWrapper to gain access to split size tuning (not used here)
 
-### 2.0.5
+## 2.0.5
+
 Very minor modifications to reduce potential issues from CPU oversubscription.
 
-### 2.0.4
+## 2.0.4
+
 Large reduction in temp space and I/O for cgpPindel.  See [cgpPindel-v2.2.0](https://github.com/cancerit/cgpPindel/releases/tag/v2.2.0)
 
-### 2.0.3
+## 2.0.3
+
 * Fixed cgpPindel
 
-### 2.0.2
+## 2.0.2
+
 * Update cgpPindel to reduce usage of Capture::Tiny apparent cause of some failures.
 
-### 2.0.1
+## 2.0.1
+
 * Test data in `examples/analysis_config.local.json` moved to a non-expiring location.
 
-### 2.0.0
+## 2.0.0
+
 * See [dockstore-cgpmap:2.0.0](https://github.com/cancerit/dockstore-cgpmap/releases/tag/2.0.0)
 * Streamlined install process to reduce build time and size of image.
 * Fix to SNV flagging - was not being applied previously.
 
-### 1.0.4
+## 1.0.4
+
 * Updates base image to add load management facilities via ENV variables.
 
-### 1.0.3
+## 1.0.3
+
 * Add params file to output bindings
 
-### 1.0.2
+## 1.0.2
+
 * Fix up output files slightly
 * Update base image for dependency (PCAP-core etc)
 
-### 1.0.1
+## 1.0.1
+
 * Fixes handling of species/assembly
 * Update base image (PCAP-core etc)
 
-### 1.0.0
+## 1.0.0
+
 Initial release of flow

Dockerfile

@@ -1,30 +1,74 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:2.0.3
+FROM  quay.io/wtsicgp/dockstore-cgpmap:3.0.1 as builder
 
-MAINTAINER  keiranmraine@gmail.com
+USER  root
 
-LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="2.1.1" \
-      description="The CGP WXS pipeline for dockstore.org"
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends\
+  locales\
+  g++\
+  make\
+  gcc\
+  pkg-config\
+  zlib1g-dev\
+  python
 
-USER  root
+# python only for building bedtools, not needed to use
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
 
 ENV OPT /opt/wtsi-cgp
-ENV PATH $OPT/bin:$PATH
+ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
 ENV LD_LIBRARY_PATH $OPT/lib
-
-ADD build/apt-build.sh build/
-RUN bash build/apt-build.sh
-
-ADD build/perllib-build.sh build/
-RUN bash build/perllib-build.sh
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
 
 ADD build/opt-build.sh build/
 RUN bash build/opt-build.sh $OPT
 
+FROM  ubuntu:16.04
+
+MAINTAINER  cgphelp@sanger.ac.uk
+
+LABEL vendor="CASM/Cancer IT, Wellcome Sanger Institute"
+LABEL uk.ac.sanger.cgp.description="CGP WXS pipeline for dockstore.org"
+LABEL uk.ac.sanger.cgp.version="3.0.0"
+
+RUN apt-get -yq update
+RUN apt-get install -yq --no-install-recommends\
+  apt-transport-https\
+  locales\
+  curl\
+  ca-certificates\
+  libperlio-gzip-perl\
+  bzip2\
+  psmisc\
+  time\
+  zlib1g\
+  liblzma5\
+  libncurses5\
+  p11-kit
+
+RUN locale-gen en_US.UTF-8
+RUN update-locale LANG=en_US.UTF-8
+
+ENV OPT /opt/wtsi-cgp
+ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
+ENV PERL5LIB $OPT/lib/perl5
+ENV LD_LIBRARY_PATH $OPT/lib
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+
+RUN mkdir -p $OPT
+COPY --from=builder $OPT $OPT
+
 ADD scripts/analysisWXS.sh $OPT/bin/analysisWXS.sh
-ADD scripts/ds-wrapper.pl $OPT/bin/ds-wrapper.pl
-RUN chmod a+x $OPT/bin/analysisWXS.sh $OPT/bin/ds-wrapper.pl
+ADD scripts/ds-cgpwxs.pl $OPT/bin/ds-cgpwxs.pl
+RUN chmod a+x $OPT/bin/analysisWXS.sh $OPT/bin/ds-cgpwxs.pl
+
+## USER CONFIGURATION
+RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
 
 USER    ubuntu
 WORKDIR /home/ubuntu