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lskatz / SneakerNet

:feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
Apache License 2.0
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Clarify/clean up CONTAINERS.md #43

Closed kapsakcj closed 4 years ago

kapsakcj commented 4 years ago

What type of PR is this?

Describe the change Lee - It will be easiest to review the changes if you visit my forked branch to see the rendered version of CONTAINERS.md instead of looking at the raw code. https://github.com/kapsakcj/SneakerNet/blob/master/docs/CONTAINERS.md

A JOSS reviewer mentioned that the CONTAINERS.md documentation wasn't easy to understand and follow (I agree! I originally originally wrote it pretty hastily!). This PR includes changes to CONTAINERS.md that clarifies instructions on using the SneakerNet docker image with both Docker and Singularity.

Importantly, it adds instructions on running the supplied example data through SneakerNet.

The commands in CONTAINERS.md were tested on PulseStar2 computer, which has the following versions of docker and singularity, but should work fine with all recent versions of each.

singularity version 3.5.2 Docker version 19.03.12, build 48a66213fe

Does it change the usage of SneakerNetPlugins.pl? no Did you add any unit testing? Please describe no

lskatz commented 4 years ago

We solved this together offline and so I am closing this PR