flowcwl

setup:

module load git
git clone --recursive https://github.com/flow-r/flowcwl

notest on setup:

installing submodules

pip install cwl-runner
# OR
git clone https://github.com/common-workflow-language/cwltool.git
cd cwltool && python setup.py install
cd cwl-runner && python setup.py install

Test

mkdir test
python cwl2script.py src/cwl2script/test/revsort.cwl src/cwl2script/test/revsort-job.json > test/revsort.sh

Notes to self

One may use use these compiled python packages (2.7.10) for linux x86_64.

module load python/2.7.10-anaconda
# compiled pkgs available here:
libdir=pythonlib/lib/python2.7/site-packages

#mkdir -p $libdir
export PYTHONPATH=`pwd`/${libdir}
python src/cwltool/setup.py install --prefix=pythonlib

extra notes (this has already been done)

# location for MDA
cd /rsrch1/genomic_med/vapor/flowcwl

git submodule add https://github.com/common-workflow-language/cwl2script src/cwl2script
git submodule add https://github.com/common-workflow-language/cwl2script src/cwltool

update submodules to latest

# http://stackoverflow.com/questions/5828324/update-git-submodule-to-latest-commit-on-origin
cd src/cwl2script
git checkout master; git pull