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update installation method for search with unit-testing
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lskatz committed Jun 5, 2024
1 parent 3df9526 commit afdff4e
Showing 1 changed file with 5 additions and 10 deletions.
15 changes: 5 additions & 10 deletions .github/workflows/unit-testing.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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