bowtie2 build fix #315
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| name: pytest | |
| on: [pull_request, push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test_mRNA: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: snakePipes/shared/rules/envs/rna_seq.yaml | |
| activate-environment: snakepipes_RNAseq_environment_3.0 | |
| condarc-file: .github/condarc.yml | |
| - name: create_starix | |
| run: | | |
| gunzip -c tests/data/genomes/genome_chr17.fa.gz > genome_chr17.fa | |
| gunzip -c tests/data/genomes/genes_chr17.gtf.gz > genes_chr17.gtf | |
| STAR --runThreadN 4 --runMode genomeGenerate --genomeDir tests/data/mRNA_STAR --genomeFastaFiles genome_chr17.fa --sjdbGTFfile genes_chr17.gtf --sjdbOverhang 100 --genomeSAindexNbases 12 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/conda_ci.yml | |
| activate-environment: conda_ci | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[actions] | |
| - name: pytest | |
| run: | | |
| snakePipes config --tempDir /tmp --condaEnvDir ./ | |
| snakePipes createEnvs --only CONDA_SHARED_ENV CONDA_RNASEQ_ENV | |
| pytest --verbosity=2 -rP tests/test_mRNA.py | |
| CI_jobcounts: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: .github/conda_ci.yml | |
| activate-environment: conda_ci | |
| condarc-file: .github/condarc.yml | |
| - name: Install snakePipes | |
| run: | | |
| pip install .[actions] | |
| - name: pytest | |
| run: | | |
| snakePipes config --tempDir /tmp --condaEnvDir ./ | |
| pytest -n 4 --verbosity=2 -rP tests/test_jobcounts.py |