Merge pull request #746 from jashapiro/743-GHA-fix-propagate

Propagate miniforge Docker changes
AlexsLemonade · Sep 3, 2024 · 4f26539 · 4f26539
2 parents f9f1386 + 67b0f5e
commit 4f26539
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Showing 5 changed files with 19 additions and 8 deletions.
diff --git a/.github/workflows/run_cell-type-ewings.yml b/.github/workflows/run_cell-type-ewings.yml
@@ -23,6 +23,7 @@ on:
     paths:
       - analyses/cell-type-ewings/**
       - "!analyses/cell-type-ewings/Dockerfile"
+      - "!analyses/cell-type-ewings/.dockerignore"
 jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'

diff --git a/.github/workflows/run_cell-type-wilms-tumor-06.yml b/.github/workflows/run_cell-type-wilms-tumor-06.yml
@@ -25,6 +25,8 @@ on:
       - main
     paths:
       - "analyses/cell-type-wilms-tumor-06/**"
+      - "!analyses/cell-type-wilms-tumor-06/Dockerfile"
+      - "!analyses/cell-type-wilms-tumor-06/.dockerignore"
 
 jobs:
   run-module:

diff --git a/.github/workflows/run_doublet-detection.yml b/.github/workflows/run_doublet-detection.yml
@@ -24,7 +24,9 @@ on:
       - main
     paths:
       - analyses/doublet-detection/**
-      - .github/workflows/run_doublet-detection.yml
+      - "!analyses/doublet-detection/Dockerfile"
+      - "!analyses/doublet-detection/.dockerignore"
+      # - .github/workflows/run_doublet-detection.yml
 
 jobs:
   run-module:
@@ -44,7 +46,7 @@ jobs:
           # Use all samples for testing unless this is triggered by a PR, in which case only use a subset of samples for faster testing
           # A single sample (or combination of samples for multiplexed data) was chosen for each ScPCA project as:
           #  Unless otherwise stated, the first sample ID in the given project
-          #  For the multiplexed project SCPCP000009, set of samples `SCPCS000133,SCPCS000134,SCPCS000135,SCPCS000136` (this group of samples has 2 associated libraries). Only `SCPCS000133` is specifed in the SAMPLES string here.
+          #  For the multiplexed project SCPCP000009, set of samples `SCPCS000133,SCPCS000134,SCPCS000135,SCPCS000136` (this group of samples has 2 associated libraries). Only `SCPCS000133` is specified in the SAMPLES string here.
           #   For the project SCPCP000011, the sample SCPCS000435 was specifically selected as an edge case sample with <10 cells
           SAMPLES: ${{ github.event_name != 'pull_request' && 'all' || 'SCPCS000001,SCPCS000024,SCPCS000050,SCPCS000101,SCPCS000124,SCPCS000133,SCPCS000168,SCPCS000216,SCPCS000246,SCPCS000250,SCPCS000298,SCPCS000435,SCPCS000481,SCPCS000484,SCPCS000490,SCPCS000502,SCPCS000514,SCPCS000616,SCPCS000632,SCPCS000758' }}
 

diff --git a/analyses/doublet-detection/Dockerfile b/analyses/doublet-detection/Dockerfile
@@ -22,9 +22,12 @@ RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/M
   && conda clean --tarballs --index-cache --packages --yes \
   && find /opt/conda -follow -type f -name '*.a' -delete \
   && find /opt/conda -follow -type f -name '*.pyc' -delete \
-  && conda clean --force-pkgs-dirs --all --yes \
-  && echo ". /opt/conda/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc \
-  && echo ". /opt/conda/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc
+  && conda clean --force-pkgs-dirs --all --yes
+
+# Activate conda environments in bash
+RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/skel/.bashrc \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
 
 # Install conda-lock
 RUN conda install --channel=conda-forge --name=base conda-lock \

diff --git a/docs/ensuring-repro/docker/docker-images.md b/docs/ensuring-repro/docker/docker-images.md
@@ -158,9 +158,12 @@ RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/M
   && conda clean --tarballs --index-cache --packages --yes \
   && find /opt/conda -follow -type f -name '*.a' -delete \
   && find /opt/conda -follow -type f -name '*.pyc' -delete \
-  && conda clean --force-pkgs-dirs --all --yes \
-  && echo ". /opt/conda/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc \
-  && echo ". /opt/conda/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc
+  && conda clean --force-pkgs-dirs --all --yes
+
+# Activate conda environments in bash
+RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/skel/.bashrc \
+  && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
 
 # Install conda-lock
 RUN conda install --channel=conda-forge --name=base conda-lock \