source .bashrc

schneebergerlab · Dec 19, 2024 · fdaa4f1 · fdaa4f1
1 parent 15a0440
commit fdaa4f1
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diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
@@ -15,6 +15,5 @@
 ## run using source to preserve alias
 #source ./example/example_workflow.sh
 
-$CONDA/bin/conda init
 $CONDA/bin/conda activate msyd
 $(tail -n +2 ./example/example_workflow.sh | sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/'  -e 's/^minimap2/.\/minimap2/' )
diff --git a/action.yml b/action.yml
@@ -34,9 +34,10 @@ runs:
     #  - name: Install other dependencies
     #    run: pip install -r requirements.txt
     #    shell: bash
-  - name: Setup conda env
+  - name: Setup conda env, install msyd
     run: |
       $CONDA/bin/conda init
+      source ~/.bashrc
       $CONDA/bin/conda env create -n msyd --file ./environment.yml
       $CONDA/bin/conda activate msyd
     shell: bash