Run PEPATAC in a container

Whether you are using docker or singularity, we have a solution to run the pipeline using containers that dramatically reduces the installation burden.

In addition to cloning the PEPATAC repository, this requires the installation and configuration of a single python package, our multi-container environment manager bulker.

Running PEPATAC using bulker

1. Install and configure bulker

Check out the bulker setup guide to install bulker on your system. It is a straightforward python package with a few configuration steps required prior to use with PEPATAC.

2. Load the PEPATAC crate

We've already produced a bulker crate for PEPATAC that requires all software needed to run the pipeline. We can load this crate directly from the bulker registry:

bulker load databio/pepatac -r

3. Activate the PEPATAC crate

Now that we've loaded the PEPATAC crate, we need to activate that specific crate so its included tools are available.

bulker activate databio/pepatac

Now, you can run any of the commands in the crate as if they were natively installed, but they're actually running in containers!

4. Run the pipeline

Now we simply run the pipeline like normal, but we wouldn't have needed to install any additional tools!

Run the pipeline at the command line

pipelines/pepatac.py --single-or-paired paired \
  --prealignments rCRSd human_repeats \
  --genome hg38 \
  --sample-name test1 \
  --input examples/data/test1_r1.fastq.gz \
  --input2 examples/data/test1_r2.fastq.gz \
  --genome-size hs \
  -O $HOME/pepatac_test

Run the pipeline using looper

Since bulker automatically direct any calls to required software to instead be executed in containers, we can just run our project the exact same way we would when we installed everything natively!

looper run examples/test_project/test_config.yaml