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update installation instructions
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lskatz committed Jun 5, 2024
1 parent 960469b commit b4fa61c
Showing 1 changed file with 2 additions and 7 deletions.
9 changes: 2 additions & 7 deletions .github/workflows/unit-testing.Listeria.Kraken1.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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