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Update makefile.yml
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skoren authored Aug 31, 2024
1 parent 19fd56b commit 3ebd4ef
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions .github/workflows/makefile.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,23 +27,23 @@ jobs:
with:
toolchain: stable

- name: Setup Python 3.10
- name: Setup Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.10.14
python-version: 3.9.19

- name: Install Conda
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
mamba-version: "*"
channels: conda-forge,bioconda
python-version: 3.10.14
python-version: 3.9.19

- name: Install dependencies
run: |
sudo apt-get update
mamba install -c conda-forge -c bioconda 'python=3.10' 'pulp<=2.7.0' 'snakemake-minimal>7,<8' 'GraphAligner>=1.0.19' 'mashmap>=3.0.6' 'winnowmap>=2.0' 'parasail-python>=1.3.3' 'networkx>=2.6.3' 'findutils>=4.6.0' 'bwa>=0.7.17' 'minimap2>=2.28' 'samtools>=1.17' biopython seqtk
mamba install -c conda-forge -c bioconda 'python=3.9' 'pulp<=2.7.0' 'snakemake-minimal>7,<8' 'GraphAligner>=1.0.19' 'mashmap>=3.0.6' 'winnowmap>=2.0' 'parasail-python>=1.3.3' 'networkx>=2.6.3' 'findutils>=4.6.0' 'bwa>=0.7.17' 'minimap2>=2.28' 'samtools>=1.17' biopython seqtk
sudo apt-get install libcurl4-openssl-dev
pip install networkx
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