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Propagate miniforge Docker changes #746

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merged 2 commits into from
Sep 3, 2024
Merged

Propagate miniforge Docker changes #746

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3b1bc64
Propagate Dockerfile changes
jashapiro Sep 3, 2024
67b0f5e
Don't run actions on docker only changes
jashapiro Sep 3, 2024
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1 change: 1 addition & 0 deletions .github/workflows/run_cell-type-ewings.yml
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Expand Up @@ -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'
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2 changes: 2 additions & 0 deletions .github/workflows/run_cell-type-wilms-tumor-06.yml
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Expand Up @@ -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:
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6 changes: 4 additions & 2 deletions .github/workflows/run_doublet-detection.yml
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Expand Up @@ -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
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I had actually added this line in at one point, see here for some context: #676

If you want to keep this line deleted for now and come back to this later, I'm fine with that!

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Yes, I know why it is there, but it would make this PR never pass, as it would keep trying to use the current docker image, not the one defined by the changes to the Dockerfile.

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Right, totally understand that, sorry if I wasn't clear! - I'm only saying if you want to wholesale delete, rather than comment out, that would be ok too.

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I think you probably want to track reverting this in an issue.

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Added this as part of #676, if that works?


jobs:
run-module:
Expand All @@ -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' }}

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9 changes: 6 additions & 3 deletions analyses/doublet-detection/Dockerfile
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Expand Up @@ -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 \
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9 changes: 6 additions & 3 deletions docs/ensuring-repro/docker/docker-images.md
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Expand Up @@ -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 \
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