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fix: check if miniconda is present before installation, closes #47 #48

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m-jahn wants to merge 4 commits into from
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fix: check if miniconda is present before installation, closes #47 #48

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2dd07a3
fix: check if miniconda is present before installation, closes #47
m-jahn Dec 4, 2025
c1be8a7
fix: change conda test file o executable
m-jahn Dec 4, 2025
17d67ca
fix: test more explicit check
m-jahn Dec 4, 2025
772c083
fix: use home env var
m-jahn Dec 4, 2025
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2 changes: 2 additions & 0 deletions action.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -74,13 +74,15 @@ runs:
EOF

- name: Setup conda
if: ${{ !hashFiles('/home/runner/miniconda3/.condarc') }}
uses: conda-incubator/setup-miniconda@v3
with:
channels: conda-forge,bioconda
channel-priority: strict
miniforge-version: latest
environment-file: .snakemake.environment.yaml
activate-environment: snakemake
installation-dir: /home/runner/miniconda3
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@ezherman ezherman Dec 4, 2025

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Here too, I believe $HOME/miniconda3 would be safer in case a self-hosted runner is used. Although is this parameter needed, which points to the default path, if we've already checked for a conda installation?


- name: Display snakemake version
shell: bash -el {0}
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