From fdaa4f1f7bf1c7e1af4326f7ecc8a073ba4cfe65 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Thu, 19 Dec 2024 16:05:40 +0800
Subject: [PATCH] source .bashrc

---
 .github/workflows/run_test_example.sh | 1 -
 action.yml                            | 3 ++-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
index 0b0412b..6332190 100755
--- 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
index 7b85aba..d8c163e 100644
--- 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