feat: gene essentiality workflow #13
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| name: Check gene essentiality with Hart 2015 | |
| on: | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "develop" | |
| jobs: | |
| check-metabolictasks: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Fetch RAVEN | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: "SysBioChalmers/RAVEN" | |
| path: "RAVEN" | |
| - name: Run gene essentiality | |
| id: essentiality | |
| run: > | |
| TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r | |
| "warning('off', 'MATLAB:rmpath:DirNotFound'); | |
| rmpath(genpath('/home/m/ecModels-dependencies/RAVEN')); | |
| rmpath(genpath('/home/m/actions-runner')); | |
| addpath(genpath('.')); | |
| setRavenSolver('gurobi'); | |
| ihuman = readYAMLmodel('model/Human-GEM.yml'); | |
| taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); | |
| [~, eGenes] = evalc('estimateEssentialGenes(ihuman, ''Hart2015_RNAseq.txt'', taskStruct);'); | |
| output = transpose(evaluateHart2015Essentiality(eGenes)); | |
| fid = fopen('data/testResults/gene-essential.csv','w'); | |
| fprintf(fid,[repmat('%s,',1,9) '%s\n'],output{:,1}); | |
| fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,5) '\n'],output{:,2:end}); | |
| fclose(fid); | |
| disp(cell2table(transpose(output(:,2:end)),"VariableNames",output(:,1)));" && | |
| PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}" && | |
| PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}" && | |
| PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}" && | |
| echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT | |
| - name: Mention PR# in README.md | |
| env: | |
| PR_NUMBER: ${{ github.event.number }} | |
| run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (gene /$PR_NUMBER\*\* (gene /" data/testResults/README.md | |
| - name: Update local branch before committing changes | |
| env: | |
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | |
| run: | | |
| git stash | |
| git fetch | |
| git checkout $BRANCH_NAME | |
| git stash pop | |
| - name: Auto-commit results | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_user_name: memote-bot | |
| commit_message: "chore: add gene essentiality test result" | |
| file_pattern: data/testResults/* | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.number }} | |
| - name: Post comment | |
| uses: NejcZdovc/comment-pr@v2 | |
| with: | |
| file: "commentGeneEssential.md" | |
| identifier: "GITHUB_COMMENT_GENE" | |
| env: | |
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | |
| TEST_RESULTS: ${{steps.essentiality.outputs.results}} | |
| GH_ACTION_RUN: ${{github.run_id}} |