diff --git a/.github/workflows/unit-testing.yml b/.github/workflows/unit-testing.yml index 7f3f800..e48046d 100644 --- a/.github/workflows/unit-testing.yml +++ b/.github/workflows/unit-testing.yml @@ -25,18 +25,13 @@ jobs: - name: apt-get install run: sudo apt-get install ca-certificates tree + - name: install-edirect run: | - sudo apt-get install ncbi-entrez-direct - echo "installed edirect the apt way" - exit - cd $HOME - perl -MNet::FTP -e '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.tar.gz");' - gunzip -cv edirect.tar.gz | tar xf - - rm -v edirect.tar.gz - export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect" - yes Y | ./edirect/setup.sh - tree edirect + sh -c "$(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 $HOME/edirect - name: check-env run: echo "$PATH" - name: download