update installation method for search with kraken2

lskatz · Jun 5, 2024 · 470398a · 470398a
1 parent afdff4e
commit 470398a
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/.github/workflows/unit-testing.Yersinia.Kraken2.yml b/.github/workflows/unit-testing.Yersinia.Kraken2.yml
@@ -34,6 +34,14 @@ jobs:
       - name: env check
         run:  |
           echo $PATH | tr ':' '\n' | sort
+
+      - name: install-edirect
+        run:  |
+          sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
+          echo $HOME/edirect >> $GITHUB_PATH
+          echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH
+          tree $HOME/edirect 
+                   
       - name: apt-get install
         run:  sudo apt-get install ca-certificates tree jellyfish ncbi-entrez-direct
       - name: select for only for this genus