diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml b/.github/workflows/unit-testing.Listeria.Kraken1.yml index f7d0367..7423e36 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -41,15 +41,10 @@ jobs: tree $(realpath .) - name: install-edirect run: | - cd $HOME - perl -MNet::FTP -e '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.tar.gz");' - gunzip -cv edirect.tar.gz | tar xf - - rm -v edirect.tar.gz + sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" echo $GITHUB_WORKSPACE/edirect >> $GITHUB_PATH echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH - #export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect" - yes Y | ./edirect/setup.sh - tree edirect + tree $GITHUB_WORKSPACE/edirect - name: check-env run: echo "$PATH" - name: select for only Listeria