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update hmtnote

Open ramprasadn opened this issue 1 year ago • 1 comments

PR checklist

This PR removes the _annotated suffix added to output files by default.

  • [ ] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
  • [ ] If necessary, include test data in your PR.
  • [ ] Remove all TODO statements.
  • [ ] Emit the versions.yml file.
  • [ ] Follow the naming conventions.
  • [ ] Follow the parameters requirements.
  • [ ] Follow the input/output options guidelines.
  • [ ] Add a resource label
  • [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • [ ] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

ramprasadn avatar Feb 13 '24 09:02 ramprasadn

I think the conda test may have failed temporarily, and rerunning might fix it.

SPPearce avatar May 02 '24 11:05 SPPearce

@ramprasadn , are you able to update this as I can't?

SPPearce avatar Jun 13 '24 20:06 SPPearce

I believe the issue lies in hmtnote's conda recipe using a post-link script to fetch an online database, which is currently down causing failures during installation. On the other hand, docker and singularity images of hmtnote already include this database locally and work without issues. I am considering having this tool exclusively run using docker and singularity containers, rather than conda.

ramprasadn avatar Jun 14 '24 14:06 ramprasadn

I believe the issue lies in hmtnote's conda recipe using a post-link script to fetch an online database, which is currently down causing failures during installation. On the other hand, docker and singularity images of hmtnote already include this database locally and work without issues. I am considering having this tool exclusively run using docker and singularity containers, rather than conda.

That is an option, if we can't get it to work on conda.

SPPearce avatar Jun 14 '24 15:06 SPPearce

@ramprasadn , do you have time to take a look at this?

SPPearce avatar Aug 23 '24 07:08 SPPearce