fix bug and update readme #34
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 SubPhaser.yaml | |
| # - name: activate | |
| # run: conda init bash | |
| # - run: cat /home/runner/.bashrc | |
| - run: conda env list | |
| - run: export PATH=/usr/share/miniconda/envs/SubPhaser/bin:$PATH | |
| # - run: . "/usr/share/miniconda/etc/profile.d/conda.sh" | |
| - run: ls -al /usr/share/miniconda/envs/SubPhaser/bin | |
| - run: which python | |
| # - run: conda activate SubPhaser | |
| - name: Install SubPhaser | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| run: export PATH=/usr/share/miniconda/envs/SubPhaser/bin:$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/SubPhaser/bin:$PATH && bash test_Arabidopsis.sh | |