conda.yml

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