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dib-lab / sourmash_plugin_pangenomics

tools for sourmash-based pangenome analyses
BSD 3-Clause "New" or "Revised" License
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MRG: add the basic code! #2

Closed ctb closed 3 months ago

ctb commented 3 months ago

Convert the basic scripts for pangenome database creation and initial analysis/extraction into plugin code, with basic adaption to the plugin class structure so that three commands run:

Taken from files over in https://github.com/dib-lab/2022-database-covers/ commit https://github.com/dib-lab/2022-database-covers/commit/1d3e8099ec65789f6515216c14b292ba79cbdff5

The subdirectory SRR5650070 contains test code that should work once the plugin is installed. To run, execute:

pip install -e .
cd SRR5650070/
snakemake -c 1
ctb commented 3 months ago

@ccbaumler all three commands run, so I'll merge and cut a release, too.

ccbaumler commented 3 months ago

[celebrate] Colton Baumler reacted to your message:

From: C. Titus Brown @.> Sent: Wednesday, May 15, 2024 2:39:18 PM To: dib-lab/sourmash_plugin_pangenomics @.> Cc: Colton Baumler @.>; Mention @.> Subject: Re: [dib-lab/sourmash_plugin_pangenomics] MRG: add the basic code! (PR #2)

@ccbaumlerhttps://github.com/ccbaumler all three commands run, so I'll merge and cut a release, too.

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