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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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Cortex dependency on stampy #150

Closed bricoletc closed 3 years ago

bricoletc commented 4 years ago

gramtools discover currently uses cortex which relies on stampy which is is python2.7.

This means that anyone that wants to install and use gramtools right now must have python2. We currently use https://github.com/iqbal-lab-org/py-cortex-api to install cortex and its dependencies. I don't want to put it up to Pypi yet because it has this 'hidden' python2 dependency.

@iqbal-lab what should we do about this? Change cortex to not use stampy? Translate the stampy code to python3?

iqbal-lab commented 4 years ago

totally happy to remove stampy from cortex and use bwa-mem for example. what would need to change?

  1. change code to call bwa (perl scrips process_calls.pl would change)
  2. change code which currently looks at SAM file, and parses the quality string, which stampy puts = in for every base where the query matches the reference in the mapped location, and instead use NM. 3/ change code which makes a stampy index of the reference to use bwa 4/ probably need to fix run_calls.pl which auto builds the stampy index for you.

Also need to check what you break in clockwork.

bricoletc commented 4 years ago

@martinghunt if you have any mental energy for this

bricoletc commented 3 years ago

https://github.com/iqbal-lab/cortex/pull/27 implements this