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

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

Cache Docker Galaxy image:

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

Generate jobs:

./scripts/pcawg_wf_gen.py --ref-download /path/to/pcawg/docstore --create-service

Submit job:

qsub sge_qsub_runworkflow.sh pcawg.service pcawg.tasks/workflow_id

To manually instance galaxy (with PCAWG Tools loaded) for interactive analysis and testing

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

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

Name		Name	Last commit message	Last commit date
Latest commit History 219 Commits
data		data
images		images
jobs		jobs
scripts		scripts
tool_data		tool_data
tools		tools
workflows		workflows
.gitignore		.gitignore
README.md		README.md
run_config.yaml		run_config.yaml
sge_qsub_runworkflow.sh		sge_qsub_runworkflow.sh