Docker builds, wrapper scripts and Galaxy tool config files related to the ICGC/TCGA PCAWG work ( http://pancancer.info/ )
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
A docker build with all of the tools needed to run the PCAP-Core scripts ( https://github.com/ICGC-TCGA-PanCancer/PCAP-core/ ).