Merge branch 'release/v3.1.0'

.travis.yml

@@ -0,0 +1,45 @@
+notifications:
+  slack: wtsi-cgpit:ptUMR1tkNyZJYd9TpGoss8WR
+  email: false
+
+env:
+ - CC=gcc
+
+addons:
+ apt:
+  packages:
+   - build-essential
+   - autoconf
+   - bsdtar
+   - time
+   - curl
+   - libcurl4-openssl-dev
+   - nettle-dev
+   - zlib1g-dev
+   - libncurses5-dev
+   - libpstreams-dev
+   - unzip
+   - libpng12-dev
+   - libexpat1-dev
+
+install: true
+
+language: perl
+
+perl:
+ - "5.22"
+
+script:
+ - git clone --depth 1 --single-branch --branch dev https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git
+ - cd PCAP-core
+ - ./setup.sh $HOME/PCAP-opt
+ - cd ../
+ - git clone --depth 1 --single-branch --branch dev https://github.com/cancerit/cgpVcf.git
+ - cd cgpVcf
+ - ./setup.sh $HOME/cgpVcf-opt $HOME/PCAP-opt/lib/perl5
+ - cd ../
+ - git clone --depth 1 --single-branch --branch dev https://github.com/cancerit/alleleCount.git
+ - cd alleleCount
+ - ./setup.sh $HOME/alleleCount-opt $HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5
+ - cd ../
+ - ./setup.sh $HOME/ascatNgs-opt $HOME/alleleCount-opt/lib/perl5:$HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5

README.md

@@ -5,6 +5,10 @@ algorithm for paired end sequencing.
 
 For details of the underlying algorithm please see the [ASCAT](https://www.crick.ac.uk/peter-van-loo/software/ASCAT) site.  The GitHub repoitory can be found [here](https://github.com/Crick-CancerGenomics/ascat).
 
+| Master | Dev |
+|---|---|
+| [![Master Build Status](https://travis-ci.org/cancerit/ascatNgs.svg?branch=master)](https://travis-ci.org/cancerit/ascatNgs) | [![Dev Build Status](https://travis-ci.org/cancerit/ascatNgs.svg?branch=dev)](https://travis-ci.org/cancerit/ascatNgs) |
+
 ---
 
 ### ASCAT core algorithm
@@ -69,4 +73,4 @@ 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/>.
+along with this program. If not, see <http://www.gnu.org/licenses/>.

perl/bin/utilities/ascatSnpPanelGenerator.pl

@@ -171,7 +171,8 @@ sub prep_outfile {
   my @raw_samples = $hts->header->text =~ m/\@RG[^\n]*[\t]SM\:([^\t\n]+)/gxms;
   die "ERROR: Input file has no 'SM' field in '\@RG' header lines\n" if(scalar @raw_samples == 0);
 
-  my @uniq_samples = keys { map {$_ => 1} @raw_samples };
+  my %tmp = map {$_ => 1} @raw_samples;
+  my @uniq_samples = keys %tmp;
   die "ERROR: Input file header indicates it contains multiple samples, '\@RG' header tag 'SM' values:\n\t".
         join(q{,},@uniq_samples)."\n" if(scalar @uniq_samples > 1);
 

perl/lib/Sanger/CGP/Ascat.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '3.0.3';
+our $VERSION = '3.1.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

setup.sh

@@ -46,13 +46,20 @@ get_file () {
   fi
 }
 
-if [ "$#" -ne "1" ] ; then
-  echo "Please provide an installation path  such as /opt/ICGC"
+if [[ ($# -ne 1 && $# -ne 2) ]] ; then
+  echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
+  echo "  ./setup.sh /opt/myBundle"
+  echo "OR all elements versioned:"
+  echo "  ./setup.sh /opt/cgpVcf-X.X.X /opt/PCAP-X.X.X/lib/perl:/some/other/lib/perl..."
   exit 0
 fi
 
 INST_PATH=$1
 
+if [[ $# -eq 2 ]] ; then
+  CGP_PERLLIBS=$2
+fi
+
 # get current directory
 INIT_DIR=`pwd`
 
@@ -85,11 +92,13 @@ PERLROOT=$INST_PATH/lib/perl5
 
 # allows user to knowingly specify other PERL5LIB areas.
 if [ -z ${CGP_PERLLIBS+x} ]; then
-  export PERL5LIB="$PERLROOT"
+  PERL5LIB="$PERLROOT"
 else
-  export PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
+  PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
 fi
 
+export PERL5LIB=$PERL5LIB
+
 #add bin path for install tests
 export PATH=$INST_PATH/bin:$PATH