docker README

.github/workflows/docker.yaml

@@ -26,9 +26,7 @@ jobs:
           cp common/docker/Dockerfile biobb_wf_godmd/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_ligand_parameterization/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_md_setup/docker/Dockerfile
-          cp common/docker/Dockerfile biobb_wf_md_setup_mutations/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_pmx_tutorial/docker/Dockerfile
-          cp common/docker/Dockerfile biobb_wf_protein_md_analysis/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_protein-complex_md_setup/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_structure_checking/docker/Dockerfile
           cp common/docker/Dockerfile biobb_wf_virtual-screening_fpocket/docker/Dockerfile

.github/workflows/readme.yaml

@@ -0,0 +1,58 @@
+on:
+  push:
+    paths:
+      - common/docker/README_common.md
+      - common/docker/README_subrepo.md
+  workflow_dispatch:
+
+name: Docker README
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          repository: bioexcel/biobb_workflows
+          path: ./
+      - name: Copy README files
+        run: |
+          cp common/docker/README_subrepo.md biobb_wf_amber_abc_setup/docker/README.md
+          cp common/docker/README_subrepo.md biobb_wf_amber_md_setup/docker/README.md
+          cp common/docker/README_subrepo.md biobb_wf_amber_md_setup_lig/docker/README.md
+          cp common/docker/README_common.md biobb_wf_cmip/docker/README.md
+          cp common/docker/README_common.md biobb_wf_dna_helparms/docker/README.md
+          cp common/docker/README_common.md biobb_wf_flexdyn/docker/README.md
+          cp common/docker/README_common.md biobb_wf_flexserv/docker/README.md
+          cp common/docker/README_common.md biobb_wf_godmd/docker/README.md
+          cp common/docker/README_common.md biobb_wf_ligand_parameterization/docker/README.md
+          cp common/docker/README_common.md biobb_wf_md_setup/docker/README.md
+          cp common/docker/README_common.md biobb_wf_pmx_tutorial/docker/README.md
+          cp common/docker/README_common.md biobb_wf_protein-complex_md_setup/docker/README.md
+          cp common/docker/README_common.md biobb_wf_structure_checking/docker/README.md
+          cp common/docker/README_subrepo.md biobb_wf_virtual-screening_fpocket/docker/README.md
+      - name: Replace placeholders in README
+        run: |
+          sed -i "s/<repository>/biobb_wf_amber/g" biobb_wf_amber_abc_setup/docker/README.md
+          sed -i "s/<subrepository>/abc_setup/g" biobb_wf_amber_abc_setup/docker/README.md
+          sed -i "s/<repository>/biobb_wf_amber/g" biobb_wf_amber_md_setup/docker/README.md
+          sed -i "s/<subrepository>/md_setup/g" biobb_wf_amber_md_setup/docker/README.md
+          sed -i "s/<repository>/biobb_wf_amber/g" biobb_wf_amber_md_setup_lig/docker/README.md
+          sed -i "s/<subrepository>/md_setup_lig/g" biobb_wf_amber_md_setup_lig/docker/README.md
+          sed -i "s/<repository>/biobb_wf_cmip/g" biobb_wf_cmip/docker/README.md
+          sed -i "s/<repository>/biobb_wf_dna_helparms/g" biobb_wf_dna_helparms/docker/README.md
+          sed -i "s/<repository>/biobb_wf_flexdyn/g" biobb_wf_flexdyn/docker/README.md
+          sed -i "s/<repository>/biobb_wf_flexserv/g" biobb_wf_flexserv/docker/README.md
+          sed -i "s/<repository>/biobb_wf_godmd/g" biobb_wf_godmd/docker/README.md
+          sed -i "s/<repository>/biobb_wf_ligand_parameterization/g" biobb_wf_ligand_parameterization/docker/README.md
+          sed -i "s/<repository>/biobb_wf_md_setup/g" biobb_wf_md_setup/docker/README.md
+          sed -i "s/<repository>/biobb_wf_pmx_tutorial/g" biobb_wf_pmx_tutorial/docker/README.md
+          sed -i "s/<repository>/biobb_wf_protein-complex_md_setup/g" biobb_wf_protein-complex_md_setup/docker/README.md
+          sed -i "s/<repository>/biobb_wf_structure_checking/g" biobb_wf_structure_checking/docker/README.md
+          sed -i "s/<repository>/biobb_wf_virtual-screening/g" biobb_wf_virtual-screening_fpocket/docker/README.md
+          sed -i "s/<subrepository>/fpocket/g" biobb_wf_virtual-screening_fpocket/docker/README.md
+      - name: Commit and push changes
+        run: |
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git add */docker/README.md && git commit -m "Updated docker README" && git push

biobb_wf_amber_abc_setup/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_abc_md_setup
+working_dir_path: biobb_wf_amber_abc_setup
 can_write_console_log: False
 run_md: False
 

biobb_wf_amber_abc_setup/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: abc_md_setup_env
+name: biobb_wf_amber
 channels:
   - conda-forge
   - bioconda

biobb_wf_amber_abc_setup/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_abc_md_setup
+working_dir_path: biobb_wf_amber_abc_setup
 can_write_console_log: False
 run_md: False
 

biobb_wf_amber_md_setup/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_amber_setup
+working_dir_path: biobb_wf_amber_md_setup
 can_write_console_log: False
 run_md: true
 

biobb_wf_amber_md_setup/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: amber_setup_env
+name: biobb_wf_amber
 channels:
   - conda-forge
   - bioconda

biobb_wf_amber_md_setup/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_amber_setup
+working_dir_path: biobb_wf_amber_md_setup
 can_write_console_log: False
 run_md: true
 

biobb_wf_amber_md_setup_lig/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_amber_complex_setup
+working_dir_path: biobb_wf_amber_md_setup_lig
 can_write_console_log: False
 run_md: false
 

biobb_wf_amber_md_setup_lig/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: amber_setup_env
+name: biobb_wf_amber
 channels:
   - conda-forge
   - bioconda

biobb_wf_amber_md_setup_lig/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_amber_complex_setup
+working_dir_path: biobb_wf_amber_md_setup_lig
 can_write_console_log: False
 run_md: false
 

biobb_wf_cmip/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_cmip
+working_dir_path: biobb_wf_cmip
 can_write_console_log: False
 run_md: true
 

biobb_wf_cmip/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: cmip_env
+name: biobb_wf_cmip
 channels:
   - conda-forge
   - bioconda

biobb_wf_cmip/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_cmip
+working_dir_path: biobb_wf_cmip
 can_write_console_log: False
 run_md: true
 

biobb_wf_dna_helparms/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_dna_helparms
+working_dir_path: biobb_wf_dna_helparms
 can_write_console_log: False
 run_md: False
 

biobb_wf_dna_helparms/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: dna_helparms_env
+name: biobb_wf_dna_helparms
 channels:
   - conda-forge
   - bioconda

biobb_wf_dna_helparms/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_dna_helparms
+working_dir_path: biobb_wf_dna_helparms
 can_write_console_log: False
 run_md: False
 

biobb_wf_flexdyn/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_flexdyn
+working_dir_path: biobb_wf_flexdyn
 can_write_console_log: False
 
 step0_extract_model:

biobb_wf_flexdyn/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: flexdyn_env
+name: biobb_wf_flexdyn
 channels:
   - conda-forge
   - bioconda

biobb_wf_flexdyn/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_flexdyn
+working_dir_path: biobb_wf_flexdyn
 can_write_console_log: False
 
 step0_extract_model:

biobb_wf_flexserv/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_flexserv
+working_dir_path: biobb_wf_flexserv
 can_write_console_log: False
 
 step0_extract_atoms:

biobb_wf_flexserv/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: flexserv_env
+name: biobb_wf_flexserv
 channels:
   - conda-forge
   - bioconda

biobb_wf_flexserv/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_flexserv
+working_dir_path: biobb_wf_flexserv
 can_write_console_log: False
 
 step0_extract_atoms:

biobb_wf_godmd/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_godmd
+working_dir_path: biobb_wf_godmd
 can_write_console_log: False
 
 step0_extract_chain:

biobb_wf_godmd/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: godmd_env
+name: biobb_wf_godmd
 channels:
   - conda-forge
   - bioconda

biobb_wf_godmd/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_godmd
+working_dir_path: biobb_wf_godmd
 can_write_console_log: False
 
 step0_extract_chain:

biobb_wf_ligand_parameterization/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_gmx_ligand_parameterization
+working_dir_path: biobb_wf_ligand_parameterization
 can_write_console_log: False
 run_md: False
 

biobb_wf_ligand_parameterization/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: ligand_parameterization_env
+name: biobb_wf_ligand_parameterization
 channels:
   - conda-forge
   - bioconda

biobb_wf_ligand_parameterization/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_gmx_ligand_parameterization
+working_dir_path: biobb_wf_ligand_parameterization
 can_write_console_log: False
 run_md: False
 

biobb_wf_md_setup/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_setup
+working_dir_path: biobb_wf_md_setup
 can_write_console_log: False
 run_md: true
 

biobb_wf_md_setup/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: setup_env
+name: biobb_wf_md_setup
 channels:
   - conda-forge
   - bioconda

biobb_wf_md_setup/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_setup
+working_dir_path: biobb_wf_md_setup
 can_write_console_log: False
 run_md: true
 

biobb_wf_md_setup_mutations/docker/Dockerfile

@@ -7,66 +7,15 @@ WORKDIR /app
 # Define a directory for the volume
 VOLUME /data
 
-# Define REPO & SUBREPO variables
-ARG REPO
-ARG SUBREPO
-
-# Check if REPO variable is set
-RUN if [ -z "$REPO" ]; then echo "REPO variable is not set. Cancelling build." && exit 1; fi
-
-# Define REPOSITORY & SUBREPOSITORY environment variables
-ENV REPOSITORY=$REPO
-ENV SUBREPOSITORY=$SUBREPO
-
-# Download the conda environment file (from the jupyter repo $REPO)
-RUN wget https://raw.githubusercontent.com/bioexcel/$REPOSITORY/main/conda_env/environment.yml -O /app/workflow.env.yml
-
-# Download the jupyter notebook file (the url varies depending on if the subrepository is set or not) and the pure python workflow file (from biobb_workflows)
-RUN if [ -z "$SUBREPOSITORY" ]; then \
-    wget https://raw.githubusercontent.com/bioexcel/$REPOSITORY/main/$REPOSITORY/notebooks/$REPOSITORY.ipynb -O /app/notebook.ipynb; \
-    wget https://raw.githubusercontent.com/bioexcel/biobb_workflows/main/$REPOSITORY/python/workflow.py -O /app/workflow.py; \
-else \
-    wget https://raw.githubusercontent.com/bioexcel/$REPOSITORY/main/$REPOSITORY/notebooks/$SUBREPOSITORY/${REPOSITORY}_$SUBREPOSITORY.ipynb -O /app/notebook.ipynb; \
-    wget https://raw.githubusercontent.com/bioexcel/biobb_workflows/main/${REPOSITORY}_$SUBREPOSITORY/python/workflow.py -O /app/workflow.py; \
-fi
+# Clone repo
+RUN wget https://raw.githubusercontent.com/bioexcel/biobb_workflows/main/biobb_wf_md_setup_mutations/python/workflow.env.yml -O /app/workflow.env.yml && \
+    wget https://raw.githubusercontent.com/bioexcel/biobb_workflows/main/biobb_wf_md_setup_mutations/python/workflow.py -O /app/workflow.py
 
 # Enable libmamba as solver
 RUN conda config --set solver libmamba
 
 # Create new environment
 RUN conda env create -f /app/workflow.env.yml
 
-# Define an environment variable with default value
-ENV MODE=python
-
-# Define environment variables for the user custom python script and jupyter notebook
-ENV USER_PY=
-ENV USER_JN=
-
-# Expose the port for the Jupyter notebook server
-EXPOSE 8888
-
-# Set the entrypoint script as the entrypoint for the Docker image
-ENTRYPOINT ["/bin/bash", "-c"]
-
-# Run either the python script or the jupyter notebook depending on the MODE environment variable
-CMD ["\
-    if [ \"$MODE\" = \"python\" ]; then \
-        if [ -n \"$USER_PY\" ]; then \
-            cp /data/\"$USER_PY\" /app/workflow.py; \
-        fi; \
-        mkdir -p /data/wf_python; \
-        cd /data/wf_python; \
-        conda run --no-capture-output -n $REPOSITORY python /app/workflow.py --config /data/workflow.yml; \
-    else \
-        mkdir -p /data/wf_notebook; \
-        if [ -n \"$USER_JN\" ]; then \
-            cp /data/\"$USER_JN\" /data/wf_notebook/notebook.ipynb; \
-        else \
-            cp /app/notebook.ipynb /data/wf_notebook/notebook.ipynb; \
-        fi; \
-        cd /data/wf_notebook; \
-        source activate $REPOSITORY; \
-        jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' --NotebookApp.password=''; \
-    fi \
-"]
+# Code to run when container is started
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "mutations_env", "python", "/app/workflow.py", "--config", "/data/workflow.yml"]

biobb_wf_md_setup_mutations/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_mutations
+working_dir_path: biobb_wf_md_setup_mutations
 can_write_console_log: False
 run_md: true
 

biobb_wf_md_setup_mutations/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: mutations_env
+name: biobb_wf_md_setup_mutations
 channels:
   - conda-forge
   - bioconda

biobb_wf_md_setup_mutations/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_mutations
+working_dir_path: biobb_wf_md_setup_mutations
 can_write_console_log: False
 run_md: true
 

biobb_wf_pmx_tutorial/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_pmx
+working_dir_path: biobb_wf_pmx_tutorial
 can_write_console_log: False
 
 mutations:

biobb_wf_protein-complex_md_setup/docker/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_complex_setup
+working_dir_path: biobb_wf_protein-complex_md_setup
 can_write_console_log: False
 run_md: false
 

biobb_wf_protein-complex_md_setup/python/workflow.env.yml

@@ -1,4 +1,4 @@
-name: complex_setup_env
+name: biobb_wf_protein-complex_md_setup
 channels:
   - conda-forge
   - bioconda

biobb_wf_protein-complex_md_setup/python/workflow.yml

@@ -1,4 +1,4 @@
-working_dir_path: wf_complex_setup
+working_dir_path: biobb_wf_protein-complex_md_setup
 can_write_console_log: False
 run_md: false