Update README.md #4
Workflow file for this run
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| name: Update MEMOTE report and model files for ESCHER maps | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - 'models/iCstr1054FB23.xml' | |
| - 'models/iCstr1197FB23.xml' | |
| - 'models/iCstr1115FB23.xml' | |
| - 'models/iCstr1116FB23.xml' | |
| - 'models/iCstrKCNa01FB23.xml' | |
| jobs: | |
| run: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: python -m pip install markupsafe==2.0.1 | |
| - name: Install dependencies ESCHER | |
| run: | | |
| python -m pip install pandas | |
| python -m pip install cobra | |
| python -m pip install escher | |
| - name: Install dependencies MEMOTE | |
| run: python -m pip install memote | |
| - name: Convert all models to json | |
| uses: jannekem/run-python-script-action@v1 | |
| with: | |
| script: | | |
| import cobra | |
| import pandas as pd | |
| model_TS = cobra.io.read_sbml_model('./models/iCstr1054FB23.xml') | |
| df_TS = pd.DataFrame.from_dict([model_TS.optimize().fluxes]).T | |
| df_TS.to_csv('./escher/iCstr1054FB23_FBA.csv') | |
| cobra.io.save_json_model(model_TS, './escher/iCstr1054FB23.json') | |
| model_1197 = cobra.io.read_sbml_model('./models/iCstr1197FB23.xml') | |
| df_1197 = pd.DataFrame.from_dict([model_1197.optimize().fluxes]).T | |
| df_1197.to_csv('./escher/iCstr1197FB23_FBA.csv') | |
| cobra.io.save_json_model(model_1197, './escher/iCstr1197FB23.json') | |
| model_1115 = cobra.io.read_sbml_model('./models/iCstr1115FB23.xml') | |
| df_1115 = pd.DataFrame.from_dict([model_1115.optimize().fluxes]).T | |
| df_1115.to_csv('./escher/iCstr1115FB23_FBA.csv') | |
| cobra.io.save_json_model(model_1115, './escher/iCstr1115FB23.json') | |
| model_1116 = cobra.io.read_sbml_model('./models/iCstr1116FB23.xml') | |
| df_1116 = pd.DataFrame.from_dict([model_1116.optimize().fluxes]).T | |
| df_1116.to_csv('./escher/iCstr1116FB23_FBA.csv') | |
| cobra.io.save_json_model(model_1116, './escher/iCstr1116FB23.json') | |
| model_KC = cobra.io.read_sbml_model('./models/iCstrKCNa01FB23.xml') | |
| df_KC = pd.DataFrame.from_dict([model_KC.optimize().fluxes]).T | |
| df_KC.to_csv('./escher/iCstrKCNa01FB23_FBA.csv') | |
| cobra.io.save_json_model(model_KC, './escher/iCstrKCNa01FB23.json') | |
| - name: Create memote report in difference mode for all models | |
| run: | | |
| memote report diff --filename "GEM_status.html" models/iCstr1054FB23.xml models/iCstr1197FB23.xml models/iCstr1115FB23.xml models/iCstr1116FB23.xml models/iCstrKCNa01FB23.xml | |
| - name: Commit ESCHER basics and memote report | |
| id: commit | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "famosab" | |
| git add --all | |
| if [-z "$(git status --porcelain)"]; then | |
| echo "::set-output name=push::false" | |
| else | |
| git commit -m "Update Memote Report and Escher basics" -a | |
| echo "::set-output name=push::true" | |
| fi | |
| - name: Push changes of the report | |
| if: steps.commit.outputs.push == 'true' | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} |