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 develop https://github.com/cancerit/cgpBigWig.git
 - cd cgpBigWig
 - ./setup.sh $HOME/PCAP-opt
 - cd ../
 - 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
 - cd ../
 - ./setup.sh $HOME/cgpPindel-opt $HOME/cgpVcf-opt $HOME/PCAP-opt

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:
 - set -e
 - export PATH=$HOME/install/bin:$HOME/install/biobambam2/bin:$PATH
 - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/cgpBigWig.git
 - cd cgpBigWig
 - ./setup.sh $HOME/PCAP-opt
 - cd ../
 - 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
 - cd ../
 - ./setup.sh $HOME/cgpPindel-opt $HOME/cgpVcf-opt $HOME/PCAP-opt

Update for fail fast and path extension for new biobambam2 install method in PCAP
Update for fail fast and path extension for new biobambam2 install method in PCAP
