From 3b1bc6431556b4c4daca367708c198874f36f829 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 13:11:55 -0400 Subject: [PATCH 1/2] Propagate Dockerfile changes --- analyses/doublet-detection/Dockerfile | 9 ++++++--- docs/ensuring-repro/docker/docker-images.md | 9 ++++++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/analyses/doublet-detection/Dockerfile b/analyses/doublet-detection/Dockerfile index 8fc6b405c..0fa44fa99 100644 --- 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 index 15e10e648..fd21343b9 100644 --- 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 \ From 67b0f5eb36da72844bed1d27983f1e4bf8c37d06 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 13:12:38 -0400 Subject: [PATCH 2/2] Don't run actions on docker only changes --- .github/workflows/run_cell-type-ewings.yml | 1 + .github/workflows/run_cell-type-wilms-tumor-06.yml | 2 ++ .github/workflows/run_doublet-detection.yml | 6 ++++-- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_cell-type-ewings.yml b/.github/workflows/run_cell-type-ewings.yml index ea66e6da3..5e06262a8 100644 --- 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 index 89eeef16b..030a04b0c 100644 --- 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 index 896b3541b..37e514e71 100644 --- 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' }}