Running individual samples in a container

Individual jobs can be run in a container by simply running the peppro.py command through docker run or singularity exec. For example, run it locally in singularity like this:

singularity exec --bind $REFGENIE $SIMAGES/peppro pipelines/peppro.py --help

With docker, you can use:

docker run --rm -it databio/peppro pipelines/peppro.py --help

Be sure to mount the volumes you need with --volume. If you're utilizing any environment variables (e.g. $REFGENIE), don't forget to include those in your docker command with the -e option.

Container details

Using docker

With docker you need to bind mount your volume that contains the pipeline and your $REFGENIE location, as well as provide the container the same environment variables your host environment is using.

In the first example, we're mounting our home user directory (/home/jps3ag/) which contains the parent directories to our $REFGENIE folder and to the pipeline itself. We'll also provide the pipeline two environment variables, $REFGENIE and $HOME.

Here's that example command in a Linux environment to run the test example through the pipeline:

docker run --rm -it --volume /home/jps3ag/:/home/jps3ag/ \
  -e REFGENIE='/home/jps3ag/genomes/genome_config.yaml' \
  -e HOME='/home/jps3ag/' \
  databio/peppro \
  /home/jps3ag/src/peppro/pipelines/peppro.py --single-or-paired single \
  --prealignments rCRSd human_repeats \
  --genome hg38 \
  --sample-name test1 \
  --input /home/jps3ag/src/peppro/examples/data/test_r1.fq.gz \
  -O $HOME/peppro_test

In this second example, we'll perform the same command in a Mac environment using Docker for Mac.

This necessitates a few minor changes to run that same example:

• replace /home/ with /Users/ format
• e.g. --volume /Users/jps3ag/:/Users/jps3ag/

Remember to allocate sufficient memory (6-8GB should generally be more than adequate) in Docker for Mac.

docker run --rm -it --volume /Users/jps3ag/:/Users/jps3ag/ \
  -e REFGENIE="/Users/jps3ag/genomes/genome_config.yaml" \
  -e HOME="/Users/jps3ag/" \
  databio/peppro \
  /Users/jps3ag/src/peppro/pipelines/peppro.py --single-or-paired single \
  --prealignments rCRSd human_repeats \
  --genome hg38 \
  --sample-name test1 \
  --input /Users/jps3ag/src/peppro/examples/data/test_r1.fq.gz \
  -O $HOME/peppro_test

Using singularity

First, build a singularity container from the docker image and create a running instance (be sure to mount your directories containing your $REFGENIE configuration file, corresponding refgenie genomes, and the pipeline.

singularity build peppro docker://databio/peppro:latest
singularity instance.start -B /home/jps3ag/:/home/jps3aq/ peppro peppro_instance

Second, run your command.

singularity exec instance://peppro_instance \
  /home/jps3ag/src/peppro/pipelines/peppro.py --single-or-paired single \
  --prealignments rCRSd human_repeats \
  --genome hg38 \
  --sample-name test1 \
  --input /home/jps3ag/src/peppro/examples/data/test_r1.fq.gz \
  -O $HOME/peppro_test

Third, close your instance when finished.

singularity instance.stop peppro_instance