Merge branch 'release/v3.3.0'

.travis.yml

@@ -19,6 +19,7 @@ addons:
     - libcairo2-dev # give png.h for kentsrc and used by R in later components
     - time
     - curl
+    - r-base-dev
 
 install: true
 
@@ -45,6 +46,8 @@ script:
  - ./setup.sh $HOME/alleleCount-opt $HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5
  - cd ../
  - ./setup.sh $HOME/cgpBattenberg-opt $HOME/alleleCount-opt/lib/perl5:$HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5
+ - cd Rsupport
+ - ./setupR.sh $HOME/cgpBattenberg-opt
 
 dist: trusty
 sudo: false

CHANGES.md

@@ -1,22 +1,38 @@
-### 3.2.2
+# Changes
+
+## 3.3.0
+
+* Upgrade to Battenberg [v2.2.8](https://github.com/Wedge-Oxford/battenberg/releases/tag/v2.2.8).
+* Upgrade to ASCAT [2.5.1](https://github.com/Crick-CancerGenomics/ascat/releases/tag/v2.5.1).
+* Docs now indicate you should run the R install scripts.
+* Email and licence updates
+
+## 3.2.2
+
 * Fix to README rendering of link
 
-### 3.2.1
+## 3.2.1
+
 * Updates to documentation
 
-### 3.2.0
+## 3.2.0
+
 * Install Battenberg R code from GitHub
 
-### 3.1.0
+## 3.1.0
+
 * Use newer alleleCount that includes faster 'dense snps' option
 * Minor modification to README.md layout
 
-### 3.0.2
+## 3.0.2
+
 * Moved call to create 1000genome loci filename hash to before use of threads to avoid glob bug in perl 5.16.3
 
-### 3.0.1
+## 3.0.1
+
 * Bug fix when there are regions which have no copynumber values set which caused bb_vcf_to_ascat_cn.pl to crash
 
-### 3.0.0
+## 3.0.0
+
 * Use verion 2.2.5 of the battenberg R package
 * Removed R files from repository

README.md

@@ -1,30 +1,63 @@
-cgpBattenberg
-=============
+# cgpBattenberg
 
-An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.
+An installation helper, perl wrapper and the R program Battenberg which detects subclonality and
+copy number in matched NGS data.
 
-| Master | Dev |
-|---|---|
-| [![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master)](https://travis-ci.org/cancerit/cgpBattenberg) | [![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=dev)](https://travis-ci.org/cancerit/cgpBattenberg) |
+| Master                                        | Develop                                         |
+| --------------------------------------------- | ----------------------------------------------- |
+| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
+
+**_This is only suitable for WGS analysis_**.
+
+<!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
+
+- [Battenberg R code](#battenberg-r-code)
+- [Docker, Singularity and Dockstore](#docker-singularity-and-dockstore)
+- [Installation](#installation)
+	- [Prerequisites](#prerequisites)
+- [Program Run Instructions](#program-run-instructions)
+
+<!-- /TOC -->
 
 ## Battenberg R code
-The Battenberg R code is developed and maintained in a separate repository [here](https://github.com/Wedge-Oxford/battenberg) and this is where any questions or issues specific to the R code should be directed.
+
+The Battenberg R code is maintained in a separate repository [Wedge-Oxford/battenberg][bb-repo]
+and this is where any questions or issues specific to the R code should be directed.
+
+## Docker, Singularity and Dockstore
+
+There is a pre-built image containing this codebase on quay.io.
+
+* [dockstore-cgpwgs][ds-cgpwgs-git]: Contains additional tools for WGS analysis.
+
+This was primarily designed for use with dockstore.org but can be used as normal containers.
+
+The docker images are know to work correctly after import into a singularity image.
 
 ## Installation
 
-The battenberg R files are installed automatically from the Battenberg GitHub repository found [here](https://github.com/Wedge-Oxford/battenberg). The linked version is currently [`v2.2.5`](https://github.com/Wedge-Oxford/battenberg/releases/tag/v2.2.5).
+The battenberg R files are installed automatically from the Battenberg GitHub repository found
+[here][bb-repo]. The linked version is currently [`v2.2.5`][bb-ver-link].
+
+Please install the following first:
+
+1. [PCAP-core v2.1.3+][pcap-core-rel]
+1. [alleleCount v3.3.1+][allele-count-rel]
+1. [cgpVcf v2.0.1+][cgpvcf-rel]
 
-Please install the following before attempting to run ``setup.sh <install_to_folder> [X/lib/perl:Y/lib/perl]``
+Then execute:
 
-1. [PCAP-core v2.1.3+](https://github.com/cancerit/PCAP-core/releases)
-2. [alleleCount v3.0.1+](https://github.com/cancerit/alleleCount/releases)
-3. [cgpVcf v2.0.1+](https://github.com/cancerit/cgpVcf/releases)
+```
+setup.sh <install_to_folder> [X/lib/perl:Y/lib/perl]
+cd Rsupport
+./setupR.sh <install_to_folder>/R-libs
+```
 
 All of the items listed here use the same install method.
 
 ### Prerequisites
 
-* Impute2 executables can be found [here](https://mathgen.stats.ox.ac.uk/impute/impute_v2.html)
+* Impute2 executables can be found [here][impute-exe]
   * Any impute related data for download
 * BWA Mapped, indexed, duplicate marked/removed bam files, for both a matched normal and tumour sample
 * Reference.fasta and index
@@ -39,23 +72,22 @@ Some required data files are not included in the distribution but a script is in
 * Prob loci file probloci.txt
   * Included: ``files/probloci.txt.gz``
 
-Additionally, the wgs_gc_correction_1000g files need to be downloaded. These can be obtained from the Battenberg R code site [here](https://github.com/Wedge-Oxford/battenberg#required-reference-files).
+Additionally, the wgs_gc_correction_1000g files need to be downloaded. These can be obtained from the Battenberg R code site [here][bb-ref].
 
 ## Program Run Instructions
 
 For the most up to date usage instructions for the wrapper code please see the command line help:
 
     battenberg.pl -h
 
-Please check the [wiki](https://github.com/cancerit/cgpBattenberg/wiki) for common problems before raising any issues.
+Please check the [wiki][cgpbb-wiki] for common problems before raising any issues.
 
-----
+# LICENCE
 
-LICENCE
-=======
-Copyright (c) 2014-2017 Genome Research Ltd.
+```
+Copyright (c) 2014-2018 Genome Research Ltd.
 
-Author: Cancer Genome Project cgpit@sanger.ac.uk
+Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 
 This file is part of cgpBattenberg.
 
@@ -81,3 +113,20 @@ 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'."
+```
+
+<!-- Travis -->
+[travis-base]: https://travis-ci.org/cancerit/cgpBattenberg
+[travis-master]: https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master
+[travis-develop]: https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=dev
+
+<!-- refs -->
+[pcap-core-rel]: https://github.com/cancerit/PCAP-core/releases
+[allele-count-rel]: https://github.com/cancerit/alleleCount/releases
+[cgpvcf-rel]: https://github.com/cancerit/cgpVcf/releases
+[impute-exe]: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
+[bb-ref]: https://github.com/Wedge-Oxford/battenberg#required-reference-files
+[cgpbb-wiki]: https://github.com/cancerit/cgpBattenberg/wiki
+[bb-repo]: https://github.com/Wedge-Oxford/battenberg
+[bb-ver-link]: https://github.com/Wedge-Oxford/battenberg/releases/tag/v2.2.5
+[ds-cgpwgs-git]: https://github.com/cancerit/dockstore-cgpwgs

Rsupport/libInstall.R

@@ -3,14 +3,39 @@ instLib = args[1]
 ascatPackage = args[2]
 battenbergPackage = args[3]
 
+#Use earier version because current version in cran is not compatible with R < 3.2 (dir.exists).
+stringi_for_legacyR = "http://cran.uk.r-project.org/src/contrib/Archive/stringi/stringi_1.1.6.tar.gz"
+
+ipak <- function(pkg){
+  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
+  if (length(new.pkg))
+    biocLite(new.pkg, ask=FALSE, lib=instLib, lib.loc=instLib)
+  sapply(pkg, library, character.only = TRUE)
+}
+
 r = getOption("repos") # hard code the UK repo for CRAN
 r["CRAN"] = "http://cran.uk.r-project.org"
 options(repos = r)
 rm(r)
-#Use previous version because current version in cran is not compatible with R < 3.2 (dir.exists).
-install.packages("http://cran.uk.r-project.org/src/contrib/Archive/stringi/stringi_1.1.2.tar.gz", repos=NULL, type="source")
-install.packages("RColorBrewer")
-install.packages("ggplot2")
-install.packages("readr")
+source("http://bioconductor.org/biocLite.R")
+
+biocPackages <- c("devtools")
+ipak(biocPackages)
+library(devtools)
+options(download.file.method = "auto")
+
+if ( version$major > 3 || ( version$major == 3 && version$minor >= 2 )) {
+  ipak(c("stringi"))
+} else {
+  install.packages(stringi_for_legacyR, repos=NULL, type="source")
+}
+
+ipak("readr")
+ipak("ggplot2")
+ipak("doParallel")
+ipak("RColorBrewer")
+ipak("gridExtra")
+ipak("gtools")
+
 install.packages(ascatPackage)
 install.packages(battenbergPackage)

Rsupport/setupR.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2017 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: Cancer Genome Project <cgpit@sanger.ac.uk>
+# Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 #
 # This file is part of BRASS.
 #
@@ -40,6 +40,9 @@ fi
 INST_PATH=$1
 BUILD_R=$2
 
+VERSION_ASCAT='2.5.1' # no 'v', not a project archive an artifact
+VERSION_BB='v2.2.8' # with 'v', this is a project archive
+
 CPU=`grep -c ^processor /proc/cpuinfo`
 if [ $? -eq 0 ]; then
   if [ "$CPU" -gt "6" ]; then
@@ -81,10 +84,10 @@ if [ "x$BUILD_R" != "x" ]; then
   cd $TMP_DIR
 fi
 
-wget https://github.com/Crick-CancerGenomics/ascat/releases/download/v2.4.3/ASCAT_2.4.3.tar.gz
-wget https://github.com/Wedge-Oxford/battenberg/archive/v2.2.5.tar.gz
+curl -sSL https://github.com/Crick-CancerGenomics/ascat/releases/download/v${VERSION_ASCAT}/ASCAT_${VERSION_ASCAT}.tar.gz > ascat_R.tar.gz
+curl -sSL https://github.com/Wedge-Oxford/battenberg/archive/$VERSION_BB.tar.gz > BB_R.tar.gz
 
-Rscript $INIT_DIR/libInstall.R $R_LIBS_USER $TMP_DIR/ASCAT_2.4.3.tar.gz $TMP_DIR/v2.2.5.tar.gz
+Rscript $INIT_DIR/libInstall.R $R_LIBS_USER ascat_R.tar.gz BB_R.tar.gz 2>&1 | grep '^\*'
 
 cd $INIT_DIR
 rm -rf $TMP_DIR

perl/Makefile.PL

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ########## LICENCE ##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: CancerIT <cgpit@sanger.ac.uk>
+# Author: CancerIT <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #

perl/bin/battenberg.pl

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2017 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: Cancer Genome Project cgpit@sanger.ac.uk
+# Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #
@@ -192,11 +192,17 @@ sub setup {
           'nl|num_loci_files=i' => \$opts{'num_loci_files'},
           'se|seed=i' => \$opts{'seed'},
           'sb|calc_seg_baf_option=i' => \$opts{'calc_seg_baf_option'},
+          'v|version' => \$opts{'version'},
 		) or pod2usage(2);
 
 	pod2usage(-verbose => 0, -exitval => 0) if(defined $opts{'h'});
   pod2usage(-verbose => 2, -exitval => 0) if(defined $opts{'m'});
 
+  if(defined $opts{'version'}) {
+    print 'Version: '.Sanger::CGP::Battenberg->VERSION,"\n";
+    exit 0;
+  }
+
   # then check for no args:
   my $defined;
   for(keys %opts) { $defined++ if(defined $opts{$_}); }
@@ -271,6 +277,10 @@ sub setup {
 		pod2usage(-msg  => "\nERROR: Invalid pr|protocol '$opts{protocol}'.\n", -verbose => 1,  -output => \*STDERR) if($bad_prot);
   }
 
+  if($opts{'reference'} !~ m/\.fai$/) {
+    warn "Automatically appending '.fai' to end of '-reference' option (see usage)\n";
+    $opts{'reference'} .= '.fai';
+  }
   PCAP::Cli::file_for_reading('reference',$opts{'reference'});
 
   my $no_of_jobs = Sanger::CGP::Battenberg::Implement::file_line_count_with_ignore($opts{'reference'},$opts{'ignored_contigs'});
@@ -471,6 +481,7 @@ =head1 SYNOPSIS
     -num_loci_files -nl Split the 1000genomes loci files into this many files. Defining a value less than the number of loci files will have no effect.
 
    Other:
+    -version  -v  Version.
     -help     -h  Brief help message.
     -man      -m  Full documentation.
 
@@ -680,4 +691,3 @@ =head1 DESCRIPTION
 B<battenberg.pl> will attempt to run all caveman steps automatically including collation of output files.
 
 =cut
-

perl/bin/battenberg_CN_to_VCF.pl

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: David Jones <cgpit@sanger.ac.uk>
+# Author: David Jones <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #

perl/bin/battenberg_version.pl

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: Cancer Genome Project cgpit@sanger.ac.uk
+# Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #

perl/bin/bb_vcf_to_ascat_cn.pl

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2016-2017 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: David Jones <cgpit@sanger.ac.uk>
+# Author: David Jones <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #

perl/bin/download_generate_bberg_ref_files.pl

@@ -1,9 +1,9 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014 Genome Research Ltd.
+# Copyright (c) 2014-2018 Genome Research Ltd.
 #
-# Author: David Jones <cgpit@sanger.ac.uk>
+# Author: David Jones <cgphelp@sanger.ac.uk>
 #
 # This file is part of cgpBattenberg.
 #