Fix bug in conda action #2
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| name: Linux bioconda | |
| on: | |
| push: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '30 10 * * *' # | |
| repository_dispatch: | |
| types: [linux-bioconda-test, install-test] | |
| jobs: | |
| x86_linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: When was this run | |
| run: date | |
| - name: configure conda | |
| run: | | |
| . $CONDA/bin/activate | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| - name: install StxTyper | |
| run: | | |
| . $CONDA/bin/activate | |
| conda install --update-deps -c conda-forge -c bioconda --strict-channel-priority -y ncbi-stxtyper | |
| stxtyper --version | |
| - name: download tests | |
| run: | | |
| BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master | |
| curl --silent --location -O ${BASE_URL}/test_stxtyper.sh | |
| - name: run tests | |
| run: | | |
| source /usr/share/miniconda/bin/activate | |
| echo CONDA_PREFIX = $CONDA_PREFIX | |
| bash ./test_stxtyper.sh path |