cwl-udocker-tests

A repository for testing udocker, cwl and toil

Step by step

Assumptions

We assume you have available:

• Installed pyenv
• Have python version 2.7.12 available
• Have exported PYENV_ROOT

We will install:

• a virtualenv for toil based on python 2.7.12
• toil v3.16.0
• udocker under your home directory
• udocker devel branch (due to problems with udocker 1.1.0's string handling and cwl)
• The udocker binaries (including a precompiled proot)

Instaling toil using pyenv

if [ ! -e $PYENV_ROOT/versions/toil ]; then
  pyenv virtualenv 2.7.12 toil
  export PYENV_VERSION=toil
  pip install -U pip setuptools wheel toil[cwl]==3.16.0
fi

Installing udocker

See install-udocker about how we do this step by step. To change the target directory export UDOCKER_BASE to another path. Otherwise we will use this directory as the base install.

git clone https://github.com/Ensembl/cwl-udocker-tests.git
cd cwl-udocker-tests
./install-udocker

Testing this has all worked

Sourcing the environment onto your

source $UDOCKER_BASE/env.sh

Setup the job (run the example Docker CWL workflow)

export TOIL_TEST=$HOME/toil-test
mkdir -p $TOIL_TEST
cd $TOIL_TEST
curl -s 'https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/examples/docker.cwl' > docker.cwl
curl -s 'https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/examples/docker-job.yml' > docker-job.yml
curl -s 'https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/examples/hello.js' > hello.js

Executing toil locally

Will create a work directory. Remove these options when in production

export TOIL_WORKDIR=$PWD/workdir-local
mkdir -p $TOIL_WORKDIR
cd $TOIL_WORKDIR
toil-cwl-runner --tmpdir-prefix $PWD --tmp-outdir-prefix $PWD --jobStore $PWD/scratch-local --clean=never --cleanWorkDir=never --user-space-docker-cmd=udocker ../docker.cwl ../docker-job.yml

Inspect the content of the workdir for output, temporary files and everything else.

Executing toil on LSF

export TOIL_WORKDIR=$PWD/workdir-lsf
mkdir -p $TOIL_WORKDIR
cd $TOIL_WORKDIR
toil-cwl-runner --batchSystem=lsf --disableCaching --tmpdir-prefix $PWD --tmp-outdir-prefix $PWD --jobStore $PWD/scratch-local --clean=never --cleanWorkDir=never --user-space-docker-cmd=udocker ../docker.cwl ../docker-job.yml