pcawg_tools

Docker builds, wrapper scripts and Galaxy tool config files related to the ICGC/TCGA PCAWG work ( http://pancancer.info/ )

Deployment

Get Nebula for deployment:

git clone https://github.com/kellrott/nebula.git

Add to PYTHONPATH:

export PYTHONPATH=`pwd`/nebula

Download Data:

cd data && ./download.sh

Obtain GATK then:

cp GenomeAnalysisTK.jar tools/gatk_bqsr/

Build Images:

python nebula/nebula/warpdrive.py build -o images/ tools/

Fetch Prebuilt Galaxy Image:

docker pull bgruening/galaxy-stable:dev

Build custom Galaxy image

git clone https://github.com/bgruening/docker-galaxy-stable.git

Then inside galaxy/Dockerfile on the apt-get line change lxc-docker to lxc-docker-1.3

Cache Docker Galaxy image:

docker save bgruening/galaxy-stable:dev > images/galaxy.tar

Manually instance galaxy (with PCAWG Tools loaded)

python nebula/nebula/warpdrive.py up -x tools/ -l data/ -a -f -w . -c

Generate jobs:

./scripts/build_jobs.py data/PCAWG_Data_Freeze_Train_2.0_Pilot_64.tsv jobs/

Submit job:

qsub sge_qsub_runworkflow.sh jobs/00ad0ffe-2105-4829-a495-1c2aceb5bb31.json workflows/Galaxy-Workflow-PCAWG_Pilot.ga

Tools

pcap_tools

A docker build with all of the tools needed to run the PCAP-Core scripts ( https://github.com/ICGC-TCGA-PanCancer/PCAP-core/ ).

contest

genetorrent

sam_pileup

delly

muse

pindel

varscan

mutect

synapse_interface