conda env create -f environment.yml
source activate bcell
yarn
Obtain a copy of the compressed input data, bcell-phylo_Ver4.tar.gz, and place in the data directory via:
mv /path/to/bcell-phylo_Ver4.tar.gz data/
After installing requirements, run the pipeline from the bcell-phylo directory:
snakemake -j $NUMBER_OF_CONCURRENT_JOBS $TARGET
Or, to distribute jobs with Sun Grid Engine:
snakemake $TARGET --cluster "qsub -V" -j $NUMBER_OF_CONCURRENT_JOBS
Make sure that the python executable for the conda environment is on your $PATH.
After running the pipeline:
yarn start
To visualize the steps of the pipeline:
yarn dag
From location where pipeline has been run (usually head node of a cluster):
rsync -arvm --include "*/V*.json" --include="*/" --exclude="*" data/ $USER@$HOST:$BCELLPHYLO/dist/data
yarn build
npx http-server -p $PORT dist