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edirect installation
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lskatz authored Jun 6, 2022
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Expand Up @@ -95,18 +95,9 @@ In addition to the installation above, please install the following.

#### Installing edirect

Modified instructions from https://www.ncbi.nlm.nih.gov/books/NBK179288/

mkdir -p ~/bin
cd ~/bin
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
$ftp->login; $ftp->binary;
$ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf -
rm edirect.tar.gz
export PATH=$PATH:$HOME/bin/edirect
./edirect/setup.sh
Modified instructions from https://www.ncbi.nlm.nih.gov/books/NBK179288/

sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"

**NOTE**: edirect needs an NCBI API key.
Instructions can be found at https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities
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