Merge pull request #744 from jashapiro/743-GHA-fix-test

Test fix for docker actions failing after miniforge
AlexsLemonade · Sep 3, 2024 · f9f1386 · f9f1386
2 parents a5b48b0 + 2a69137
commit f9f1386
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diff --git a/.github/workflows/run_cell-type-ewings.yml b/.github/workflows/run_cell-type-ewings.yml
@@ -22,6 +22,7 @@ on:
       - main
     paths:
       - analyses/cell-type-ewings/**
+      - "!analyses/cell-type-ewings/Dockerfile"
 jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'

diff --git a/analyses/cell-type-ewings/Dockerfile b/analyses/cell-type-ewings/Dockerfile
@@ -35,9 +35,12 @@ 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
 
 # add conda-lock
 RUN conda install conda-lock && conda clean --all --yes