switch to modifying code at runtime

schneebergerlab · Dec 12, 2024 · 582d111 · 582d111
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commit 582d111
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Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
@@ -4,12 +4,16 @@
 # hacky way to hopefully alias the calls
 # normal alias does not seem to work in GitHub CI
 # necessary, as the hacky git install does not install the CLI entrypoints
-echo "#!/bin/bash python <(echo 'import syri.scripts.syri;syri.scripts.syri.main()')" > syri
-chmod +x ./syri
-echo "minimap2.py" > ./minimap2
-chmod +x ./minimap2
-PATH=$PATH:./
-syri --version
-minimap2
-# run using source to preserve alias
-source ./example/example_workflow.sh
+#echo "python <(echo 'import syri.scripts.syri;syri.scripts.syri.main()')" > syri
+#chmod +x ./syri
+#echo "minimap2.py" > ./minimap2
+#chmod +x ./minimap2
+#PATH=$PATH:./
+#syri --version
+#minimap2
+## run using source to preserve alias
+#source ./example/example_workflow.sh
+
+$CONDA/bin/conda install -c conda-forge -c bioconda "bioconda::minimap2"
+$(tail -n -1 ./example/example_workflow.sh |\
+	sed -e 's/^syri/python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")/' )
diff --git a/.github/workflows/test_example.yml b/.github/workflows/test_example.yml
@@ -23,7 +23,7 @@ jobs:
         python-version: "3.12"
     - name: Install other tools using conda
       run: |
-        $CONDA/bin/conda install -c conda-forge -c bioconda "minimap2"
+        $CONDA/bin/conda install -c conda-forge -c bioconda "bioconda::minimap2"
     - name: Test example_run.sh
       run: ./.github/workflows/run_test_example.sh
       shell: bash