Merge branch 'release/1.0.0'

Dockerfile

@@ -3,12 +3,11 @@ FROM  ubuntu:16.04
 MAINTAINER  [email protected]
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="0.0" \
-      description="The CGP mapping pipeline 'in-a-box'"
+      version="1.0.0" \
+      description="The CGP mapping pipeline for dockstore.org"
 
 USER  root
 
-ENV CGPBOX_VERSION $cgpbox_ver
 ENV OPT /opt/wtsi-cgp
 ENV PATH $OPT/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
@@ -19,15 +18,18 @@ RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir
 RUN mkdir -p $OPT/bin
 
 ADD scripts/mapping.sh $OPT/bin/mapping.sh
-RUN chmod a+x $OPT/bin/mapping.sh
+ADD scripts/ds-wrapper.pl $OPT/bin/ds-wrapper.pl
+RUN chmod a+x $OPT/bin/mapping.sh $OPT/bin/ds-wrapper.pl
 
 ADD build/apt-build.sh build/
+ADD build/perllib-build.sh build/
 ADD build/opt-build.sh build/
 
 RUN bash build/apt-build.sh
+RUN bash build/perllib-build.sh
 RUN bash build/opt-build.sh
 
 USER    ubuntu
 WORKDIR /home/ubuntu
 
-ENTRYPOINT /bin/bash
+CMD ["/bin/bash"]

Dockstore.cwl

@@ -0,0 +1,100 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+id: "cgpmap"
+label: "CGP BWA-mem mapping flow"
+cwlVersion: v1.0
+doc: |
+    ![build_status](https://quay.io/repository/cancerit/dockstore-cgpmap/status)
+    A Docker container for the CGP BWA-mem mapping flow. See the [dockstore-cgpmap](https://github.com/cancerit/dockstore-cgpmap) website for more information.
+
+dct:creator:
+  "@id": "http://orcid.org/0000-0002-5634-1539"
+  foaf:name: Keiran M Raine
+  foaf:mbox: "mailto:keiranmraine@gmail.com"
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpmap:1.0.0"
+
+hints:
+  - class: ResourceRequirement
+    coresMin: 1 # works but long, 8 recommended
+    ramMin: 15000 # good for WGS human ~30-60x
+    outdirMin: 5000000 # unlikely any BAM processing would be possible in less
+
+inputs:
+  reference:
+    type: File
+    doc: "The core reference (fa, fai, dict) as tar.gz"
+    inputBinding:
+      prefix: -reference
+      position: 1
+      separate: true
+
+  bwa_idx:
+    type: File
+    doc: "The BWA indexes in tar.gz"
+    inputBinding:
+      prefix: -bwa_idx
+      position: 2
+      separate: true
+
+  sample:
+    type: string
+    doc: "Sample name to be included in output [B|CR]AM header, also used to name final file"
+    inputBinding:
+      prefix: -sample
+      position: 3
+      separate: true
+
+  scramble:
+    type: string?
+    doc: "Options to pass to scramble when generating CRAM output, see scramble docs"
+    default: ''
+    inputBinding:
+      prefix: -scramble
+      position: 4
+      separate: true
+      shellQuote: true
+
+  bwa:
+    type: string?
+    default: ' -Y -K 100000000'
+    doc: "Mapping and output parameters to pass to BWA-mem, see BWA docs, default ' -Y -K 100000000'"
+    inputBinding:
+      prefix: -bwa
+      position: 5
+      separate: true
+      shellQuote: false
+
+  cram:
+    type: boolean
+    doc: "Set if output should be in CRAM format instead of BAM, see 'scramble' for tuning parameters."
+    inputBinding:
+      prefix: -cram
+      position: 6
+
+  bams_in:
+    type:
+    - 'null'
+    - type: array
+      items: File
+    doc: "Can be BAM, CRAM, fastq (paired or interleaved), BAM/CRAM can be mixed together but not FASTQ."
+    inputBinding:
+      position: 7
+
+outputs:
+  mapped_out:
+    type: File
+    outputBinding:
+      glob: $(inputs.sample).bam
+    secondaryFiles:
+      - .bai
+      - .bas
+      - .md5
+      - .met
+      - .maptime
+
+
+baseCommand: ["/opt/wtsi-cgp/bin/ds-wrapper.pl"]

README.md

@@ -0,0 +1,46 @@
+dockstore-cgpmap
+======
+`dockstore-cgpmap` provides a complete multi threaded BWA mem mapping workflow.  This has been packaged specifically for use with the [Dockstore.org](https://dockstore.org/) framework.
+
+Supports input in following formats:
+* Multiple BAM
+* Multiple CRAM
+* Multiple fastq[.gz] (paired or interleaved)
+  * Please see [PCAP-core/bin/bwa_mem.pl](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/blob/master/bin/bwa_mem.pl) for formatting of file names.
+
+Options for customisation:
+
+* BWA specific mapping parameters (defaults are based on attempts at a global standard).
+* Optionally ouput CRAM (scramble parameters can be modified)
+
+LICENCE
+=======
+
+Copyright (c) 2016 Genome Research Ltd.
+
+Author: Cancer Genome Project <[email protected]>
+
+This file is part of dockstore-cgpmap.
+
+dockstore-cgpmap is free software: you can redistribute it and/or modify it under
+the terms of the GNU Affero General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option) any
+later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+1. The usage of a range of years within a copyright statement contained within
+this distribution should be interpreted as being equivalent to a list of years
+including the first and last year specified and all consecutive years between
+them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
+2009, 2011-2012’ should be interpreted as being identical to a statement that
+reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
+statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
+identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
+2009, 2010, 2011, 2012’."

build/apt-build.sh

@@ -7,7 +7,6 @@ apt-get -yq install apt-transport-https
 apt-get -yq install autoconf
 apt-get -yq install bsdtar
 apt-get -yq install build-essential
-apt-get -yq install ca-certificates
 apt-get -yq install curl
 apt-get -yq install libboost-dev
 apt-get -yq install libboost-iostreams-dev
@@ -21,17 +20,15 @@ apt-get -yq install libpstreams-dev
 apt-get -yq install libreadline6-dev
 apt-get -yq install libssl-dev
 apt-get -yq install nettle-dev
-apt-get -yq install nfs-common
 apt-get -yq install python-software-properties
-apt-get -yq install s3cmd
-apt-get -yq install software-properties-common
 apt-get -yq install unzip
 apt-get -yq install time
 apt-get -yq install zlib1g-dev
 apt-get -yq install libpam-tmpdir
 apt-get -yq install libcairo2-dev
 
 ### security upgrades and cleanup
+apt-get -yq install unattended-upgrades
 unattended-upgrades
 apt -yq autoremove
 apt-get clean

build/opt-build.sh

@@ -26,22 +26,4 @@ cd /tmp/downloads/distro
 cd /tmp/downloads
 rm -rf distro.zip /tmp/downloads/distro /tmp/hts_cache
 
-# alleleCount
-curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/alleleCount/archive/v3.2.1.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
-./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro
-
-# cgpNgsQc
-curl -sSL -o distro.zip --retry 10 https://github.com/cancerit/cgpNgsQc/archive/v1.3.0.zip
-mkdir /tmp/downloads/distro
-bsdtar -C /tmp/downloads/distro --strip-components 1 -xf distro.zip
-cd /tmp/downloads/distro
-./setup.sh $OPT
-cd /tmp/downloads
-rm -rf distro.zip /tmp/downloads/distro
-
 rm -rf /tmp/downloads

build/perllib-build.sh

@@ -0,0 +1,104 @@
+#!/bin/bash
+
+set -eux
+
+apt-get -yq update
+# install all perl libs, identify by grep of cgp_box_stack build "grep 'Successfully installed' build_stack.log"
+# much faster, items needing later versions will still upgrade
+# still install those that get an upgrade though as dependancies will be resolved
+
+## command to parse a build output before applying package based install
+## some will need editign still
+#grep '^Successfully installed ' build.log | perl -ne 's/ [(].+$/\n/;s/^.+ //;s/[-][^-]+$//;printf qq{apt-get -yq install lib%s-perl\n},lc $_;'
+
+## commented items are up-to-date
+apt-get -yq install libextutils-cbuilder-perl
+apt-get -yq install libmodule-build-perl
+apt-get -yq install libextutils-config-perl
+apt-get -yq install libextutils-installpaths-perl
+apt-get -yq install libextutils-helpers-perl
+apt-get -yq install libmodule-build-tiny-perl
+apt-get -yq install libfile-sharedir-install-perl
+apt-get -yq install libclass-inspector-perl
+apt-get -yq install libfile-sharedir-perl
+#apt-get -yq install libsub-exporter-progressive-perl
+apt-get -yq install libconst-fast-perl
+apt-get -yq install libfile-which-perl
+#apt-get -yq install libhtml-tagset-perl
+#apt-get -yq install libhtml-parser-perl
+#apt-get -yq install libencode-locale-perl
+#apt-get -yq install liblwp-mediatypes-perl
+#apt-get -yq install libhttp-date-perl
+#apt-get -yq install libio-html-perl
+#apt-get -yq install liburi-perl
+#apt-get -yq install libhttp-message-perl
+apt-get -yq install libhttp-cookies-perl
+apt-get -yq install libhttp-negotiate-perl
+apt-get -yq install libhttp-daemon-perl
+apt-get -yq install libfile-listing-perl
+apt-get -yq install libwww-robotrules-perl
+apt-get -yq install libnet-http-perl
+apt-get -yq install libwww-perl
+apt-get -yq install libtest-deep-perl
+apt-get -yq install libdevel-stacktrace-perl
+apt-get -yq install libclass-data-inheritable-perl
+apt-get -yq install libexception-class-perl
+apt-get -yq install libsub-uplevel-perl
+apt-get -yq install libtest-exception-perl
+apt-get -yq install libtest-simple-perl
+apt-get -yq install libcapture-tiny-perl
+apt-get -yq install libtext-diff-perl
+apt-get -yq install libtest-differences-perl
+apt-get -yq install libtest-warn-perl
+apt-get -yq install libtest-most-perl
+apt-get -yq install libio-string-perl
+apt-get -yq install libdata-stag-perl
+apt-get -yq install libbio-perl-perl
+apt-get -yq install libtest-leaktrace-perl
+apt-get -yq install libappconfig-perl
+apt-get -yq install libtemplate-perl
+apt-get -yq install liblog-message-perl
+apt-get -yq install liblog-message-simple-perl
+apt-get -yq install libterm-ui-perl
+apt-get -yq install libdevel-cover-perl
+#apt-get -yq install libio-stringy-perl
+apt-get -yq install libconfig-inifiles-perl
+#apt-get -yq install libtry-tiny-perl
+#apt-get -yq install libdevel-symdump-perl
+apt-get -yq install libpod-coverage-perl
+#apt-get -yq install libparams-util-perl
+apt-get -yq install libtest-nowarnings-perl
+#apt-get -yq install libclone-perl
+apt-get -yq install libhook-lexwrap-perl
+apt-get -yq install libtest-subcalls-perl
+#apt-get -yq install libexporter-tiny-perl
+apt-get -yq install libxsloader-perl
+#apt-get -yq install liblist-moreutils-perl
+apt-get -yq install libfile-remove-perl
+apt-get -yq install libtest-object-perl
+#apt-get -yq install libtask-weaken-perl
+apt-get -yq install libppi-perl
+apt-get -yq install libcss-tiny-perl
+apt-get -yq install libppi-html-perl
+apt-get -yq install libversion-perl
+apt-get -yq install libdata-uuid-perl
+apt-get -yq install libipc-system-simple-perl
+apt-get -yq install libproc-processtable-perl
+#apt-get -yq install libxml-sax-base-perl
+#apt-get -yq install libxml-namespacesupport-perl
+#apt-get -yq install libxml-sax-perl
+#apt-get -yq install libxml-parser-perl
+#apt-get -yq install libxml-sax-expat-perl
+#apt-get -yq install libxml-simple-perl
+apt-get -yq install libcanary-stability-perl
+apt-get -yq install libcommon-sense-perl
+apt-get -yq install libtypes-serialiser-perl
+apt-get -yq install libjson-xs-perl
+apt-get -yq install libproc-pid-file-perl
+apt-get -yq install libtest-fatal-perl
+apt-get -yq install libjson-perl
+
+### security upgrades and cleanup
+unattended-upgrades
+apt -yq autoremove
+apt-get clean