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MAINT: updates env file names#170

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gregcaporaso merged 2 commits into
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rachis-migration-support
Apr 17, 2026
Merged

MAINT: updates env file names#170
gregcaporaso merged 2 commits into
mainfrom
rachis-migration-support

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@lizgehret
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@lizgehret lizgehret commented Apr 17, 2026

hey @gregcaporaso i started with just the environment file names and then realized we needed a slightly bigger update to accommodate the qiime2 -> rachis and amplicon -> qiime2 name changes. this still needs more work, but i'll add to it when i'm back in the office on tuesday.


AI DISCLOSURE: no AI was used.

@lizgehret lizgehret changed the title updates env files & handles amplicon -> qiime2 -> rachis MAINT: updates env files & handles amplicon -> qiime2 -> rachis Apr 17, 2026
Co-Authored-By: Liz Gehret <elizabeth.gehret@gmail.com>
@gregcaporaso gregcaporaso force-pushed the rachis-migration-support branch from 81adee1 to 059523d Compare April 17, 2026 20:37
@gregcaporaso gregcaporaso changed the title MAINT: updates env files & handles amplicon -> qiime2 -> rachis MAINT: updates env file names Apr 17, 2026
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gregcaporaso commented Apr 17, 2026

@lizgehret, as discussed offline, I split the general name changes off into #171. This one now just updates the dev environment install instructions. I'll test those and merge if it's working, and you and I can discuss the approach for #171.

Update:

  • amplicon and tiny installed using the commands here on macOS
  • pathogenome failed on linux (monsoon)
  • moshpit installed using the commands here on linux

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I'm going to merge this. Let me know if you need additional testing of pathogenome @lizgehret.

@gregcaporaso gregcaporaso merged commit 285ff1a into main Apr 17, 2026
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3 participants