actions

.github/workflows/main.yml

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+# 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
+