chore: update model I/O functions and documentation #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
| name: Check gene essentiality with Hart 2015 | |
| on: | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "develop" | |
| jobs: | |
| gene-essentiality: | |
| 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=$(/usr/local/bin/matlab -batch | |
| "warning('off', 'MATLAB:rmpath:DirNotFound'); | |
| rmpath(genpath('/home/m/ecModels-dependencies/RAVEN')); | |
| rmpath(genpath('/home/m/actions-runner')); | |
| addpath(genpath('.')); | |
| setRavenSolver('gurobi'); | |
| ihuman = readYAMLmodel('model/Human-GEM.yml'); | |
| taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); | |
| [~, eGenes] = evalc('estimateEssentialGenes(ihuman, ''Hart2015_RNAseq.txt'', taskStruct);'); | |
| output = transpose(evaluateHart2015Essentiality(eGenes)); | |
| fid = fopen('data/testResults/gene-essential.csv','w'); | |
| fprintf(fid,[repmat('%s,',1,9) '%s\n'],output{:,1}); | |
| fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,5) '\n'],output{:,2:end}); | |
| fclose(fid); | |
| disp(cell2table(transpose(output(:,2:end)),'VariableNames',output(:,1)));") && | |
| echo "$TEST_RESULTS" && | |
| PARSED_RESULTS="${TEST_RESULTS//$'\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 | |
| if git stash list | grep -q 'stash@{'; then | |
| git stash pop | |
| fi | |
| - 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}} |