From d1d6e0ce97c8832ff7a470028e761645e763eb26 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Thu, 12 Dec 2024 15:01:07 +0800
Subject: [PATCH] try specifying bash shell

---
 .github/workflows/run_test_example.sh | 5 +++--
 .github/workflows/test_example.yml    | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
index 13a4a5e..4fce6a2 100755
--- a/.github/workflows/run_test_example.sh
+++ b/.github/workflows/run_test_example.sh
@@ -2,10 +2,11 @@
 
 # alias to a call launching the syri entrypoint from python
 # necessary, as the hacky git install does not install the CLI entrypoints
-alias syri='python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")'
+alias syri="python <(echo 'import syri.scripts.syri;syri.scripts.syri.main()')"
+alias minimap2="python <(echo 'import syri.scripts.syri;syri.scripts.syri.main()')"
 python <(echo "import syri.scripts.syri;syri.scripts.syri.main()") --version
 syri --version
 minimap2 --version
-minimap2.py --version
+minimap2.py
 # run using source to preserve alias
 source ./example/example_workflow.sh
diff --git a/.github/workflows/test_example.yml b/.github/workflows/test_example.yml
index 4ab148c..27a068d 100644
--- a/.github/workflows/test_example.yml
+++ b/.github/workflows/test_example.yml
@@ -26,3 +26,4 @@ jobs:
         $CONDA/bin/conda install -c conda-forge -c bioconda "minimap2"
     - name: Test example_run.sh
       run: ./.github/workflows/run_test_example.sh
+      shell: bash