Functionmotifs #197
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| name: CI | |
| # specify trigger events for ci workflow | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| types: [opened, edited, reopened, synchronize, review_requested] | |
| jobs: | |
| # apply formating and linting | |
| Format: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Apply snakefmt | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| LINTER_RULES_PATH: snekmer/rules/ | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| # run all tests | |
| Test: | |
| runs-on: ubuntu-20.04 | |
| needs: | |
| - Format | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build test environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: anaconda,conda-forge,bioconda,numba | |
| auto-activate-base: false | |
| activate-environment: snekmer | |
| environment-file: .test/test-env.yml | |
| - shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show | |
| - shell: bash -l {0} | |
| run: mamba install -y -c conda-forge snakemake==7.0 tabulate==0.8.10 | |
| - shell: bash -l {0} | |
| run: pip install -e git+https://github.com/PNNL-CompBio/Snekmer@functionmotifs#egg=snekmer | |
| #test clustering step | |
| - name: Snekmer Cluster | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| conda info --envs | |
| source activate snekmer | |
| conda config --get channel_priority --json | |
| snekmer cluster --configfile .test/config.yaml -d .test | |
| rm -rf .test/output | |
| # --use-conda --conda-cleanup-pkgs cache --show-failed-logs --conda-frontend mamba | |
| # run modeling step and move output files for search | |
| - name: Snekmer Model | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate snekmer | |
| snekmer model --configfile .test/config.yaml -d .test --cores 1 | |
| mkdir .test/output/example-model | |
| mv .test/output/model/*.model .test/output/example-model/ | |
| mv .test/output/kmerize/*.kmers .test/output/example-model/ | |
| mv .test/output/scoring/*.scorer .test/output/example-model/ | |
| # search against previously generated model files | |
| - name: Snekmer Search | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate snekmer | |
| ls .test | |
| pwd | |
| snekmer search --configfile .test/config.yaml -d .test --cores 1 | |
| rm -rf .test/output | |
| # run Snekmer Learn kmer counts and confidence creation | |
| - name: Snekmer Learn | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate snekmer | |
| snekmer learn --configfile .test/config_learnapp.yaml -d .test --cores 1 | |
| mkdir .test/counts .test/confidence | |
| mv .test/output/learn/kmer-counts-total.csv .test/counts/kmer-counts-total.csv | |
| mv .test/output/eval_conf/global-confidence-scores.csv .test/confidence/global-confidence-scores.csv | |
| rm -rf .test/output | |
| # run Snekmer Learn against previously generated counts files | |
| - name: Snekmer Apply | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate snekmer | |
| snekmer apply --configfile .test/config_learnapp.yaml -d .test --cores 1 | |
| rm -rf .test/output | |
| # run Snekmer Motif using previously generated model files | |
| - name: Snekmer Motif | |
| run: | | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate snekmer | |
| snekmer motif --configfile .test/config.yaml -d .test --cores 1 | |
| rm -rf .test/output |