main.yml

# This is a basic workflow to help you get started with Actions

name: CI

# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the master branch
on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
    - name: Install dependencies
    # set up conda
      uses: s-weigand/setup-conda@v1.0.5
#      with:
#        conda-channels: bioconda
    - uses: actions/checkout@v2
    # install dependencies
    - run: conda env create -f OrthoIndex.yaml

#    - name: activate
#      run: conda init bash
#    - run: cat /home/runner/.bashrc
    - run: conda env list
    - run: export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH
#    - run: . "/usr/share/miniconda/etc/profile.d/conda.sh"
    - run: ls -al /usr/share/miniconda/envs/OrthoIndex/bin
    - run: which python   
#    - run: conda activate SubPhaser
      
    - name: Install OrthoIndex
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      run: export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH && python setup.py install
    
#    - name: run test
    # run test 
#      run: cd example_data
    - run: ls -al
    - run: pwd
    - run: cd example_data && export PATH=/usr/share/miniconda/envs/OrthoIndex/bin:$PATH && bash example.sh