%appinstall workflow-toil
apt update -y --fix-missing
apt install -y wget bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 git mercurial subversion
MINICONDAURL=https://repo.continuum.io/miniconda/Miniconda3-4.3.30-Linux-x86_64.sh
wget --quiet ${MINICONDAURL} -O miniconda.sh
/bin/bash miniconda.sh -b -p miniconda
rm miniconda.sh
PATH=/scif/apps/workflow-toil/miniconda/bin:$PATH
export PATH
/scif/apps/workflow-toil/miniconda/bin/conda install -y --channel bioconda --channel glaxosmithkline python=2.7.14 cwltool=1.0.20170928192020 typing=3.5.3.0
%appfiles workflow-toil
%appenv workflow-toil
CWLTOOL_HOME=/scif/apps/workflow-toil
export CWLTOOL_HOME
PATH=/scif/apps/workflow-toil/miniconda/bin:$PATH
export PATH
%apphelp workflow-toil
Scalable, efficient, cross-platform pipeline management system, written
entirely in Python, and designed around the principles of functional
programming
It is recommended to create the following aliases:
alias toil="singularity run --app workflow-toil \${SINGULARITY_CONTAINER}"
alias cwltoil="singularity exec --app workflow-toil \${SINGULARITY_CONTAINER} cwltoil"
alias cwltool="singularity exec --app workflow-toil \${SINGULARITY_CONTAINER} cwltool"
More help is then available by running
toil --help
%apprun workflow-toil
toil "$@"
%applabels workflow-toil
MAINTAINER adomissy@ucsd.edu
BUILD_VERSION 0.0.1
WRAPPEDTOOL_VERSION 3.11.0
WRAPPEDTOOL_INFO http://toil.ucsc-cgl.org/