try updating base env instead

schneebergerlab · Dec 19, 2024 · 04a8ce2 · 04a8ce2
1 parent fdaa4f1
commit 04a8ce2
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diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
@@ -15,5 +15,5 @@
 ## run using source to preserve alias
 #source ./example/example_workflow.sh
 
-$CONDA/bin/conda activate msyd
+#$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
@@ -36,10 +36,11 @@ runs:
     #    shell: bash
   - name: Setup conda env, install msyd
     run: |
-      $CONDA/bin/conda init
-      source ~/.bashrc
-      $CONDA/bin/conda env create -n msyd --file ./environment.yml
-      $CONDA/bin/conda activate msyd
+      #$CONDA/bin/conda init
+      #source ~/.bashrc
+      #$CONDA/bin/conda env create -n msyd --file ./environment.yml
+      #$CONDA/bin/conda activate msyd
+      conda env update -n base --file ./environment.yml
     shell: bash
     # python -m pip install mappy
   - name: Build msyd