From 470398aaa59ed120d23c982dd54df70b093711bf Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Wed, 5 Jun 2024 14:48:27 -0400 Subject: [PATCH] update installation method for search with kraken2 --- .github/workflows/unit-testing.Yersinia.Kraken2.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/unit-testing.Yersinia.Kraken2.yml b/.github/workflows/unit-testing.Yersinia.Kraken2.yml index d695e66..bae8dff 100644 --- 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