Setup Notes

NOTE: this setup is of limited use without auxiliary components i.e. our specialized MongoDB setup used for logging and tracking

Create a snakemake environment with needed components:
- ver=3.7.1; conda create -n snakemake-$ver pymongo drmaa python-dateutil snakemake=$ver -c bioconda
- Change snakemake_env in etc/site.yaml to point to this env
Install other components into conda root env:
- conda install pymongo drmaa yaml pylint python-dateutil
Install pymongo into conda root env
Create testing and logging directories per pipeline (see tools/create_pipeline_dirs.sh)
Software/modules management is based on dotkit. See also lib/pipelines.py:INIT
Test scripts expect RPD_ROOT to be set
ELM logging goes to RPD_ELMLOGDIR

Install Preview

src=pipelines.git/
pushd $src; vstr=$(git rev-parse --short HEAD); popd
dest=pipelines-preview/pipelines-$vstr
rsync -av --exclude '.git/' --exclude '*~' --exclude '/tmp/' --exclude 'etc/' --exclude '*/_*' --exclude '*.check.*' $src/ $dest
set interpreter in shebang of $dest/run
mkdir $dest/etc
copy yaml of choice to $dest/etc/ and link site.yaml