Run in a container
Whether you are using
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
1. Install and configure
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
2. Load the
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 load databio/pepatac -r
3. Activate the
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
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