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[WIP] Implement easier singularity compatibility#166

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dnwissel:singularity
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[WIP] Implement easier singularity compatibility#166
dnwissel wants to merge 2 commits into
sheynkman-lab:mainfrom
dnwissel:singularity

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Description

Implements methods to make it easier to run the LRP pipeline on singularity via a proteowizard sandbox.

Changes:

  1. Enable --writable-tmpfs for wine ([singularity] Adding --writable-tmpfs option to selected containers for Singularity compatibility #165)
  2. Use a proteowizard sandbox for running wine on singularity (Docker to Singularity for HPC and permissions ProteoWizard/pwiz#2387 (comment))
  3. Implement bash scripts to easily switch between docker and singularity (sandbox isn't actually online yet, we need to add it to Zenodo or similar later on)

Documentation etc will be added once this has been verified to work on other systems/clusters. I have already verified this on two of my systems.

PR checklist

  • This comment contains a description of changes (with reason)
  • [] CHANGELOG.md is updated
  • [] If you've fixed a bug or added code that should be tested, add tests!
  • [] Documentation in docs is updated

Let me know if you have any feedback, this is still WIP to some extent.

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