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#!/bin/bash -norc
DIR="$( cd "$( dirname "$0" )" && pwd )"
cat <<EOF
Trying to establish local installations of any missing Perl modules
(as logged in $DIR/setup-deps.log).
Please be patient, as this step may take a little while.
EOF
cd "$DIR"
mkdir -p _cpan/CPAN
echo '1;' >> _cpan/CPAN/MyConfig.pm
if ! perl -I_cpan -Iaux/lib/perl5 setup-deps.pl </dev/null >setup-deps.log 2>&1
then
if grep '^read timeout.*HTTP' setup-deps.log >/dev/null
then
cat <<EOF
Unable to access the Comprehensive Perl Archive Network. You might
need to set http_proxy and/or ftp_proxy in your user environment.
Please consult your network administrator for suitable values.
EOF
fi
fi
rm -rf _cpan
if ! perl -Iaux/lib/perl5 -MMozilla::CA -e '1;' 2>/dev/null
then
gzip -cd Mozilla-CA.tar.gz | tar xvf -
fi
osname=`uname -s | sed -e 's/_NT-.*$/_NT/; s/^MINGW[0-9]*/CYGWIN/'`
cputype=`uname -m`
case "$osname-$cputype" in
Linux-x86_64 | Darwin-x86_64 | CYGWIN_NT-* )
./ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract."$osname".gz
gunzip -f xtract."$osname".gz
;;
esac
if [ -f xtract."$osname" ]
then
chmod +x xtract."$osname"
else
echo "Unable to download a prebuilt xtract executable; attempting to"
echo "build one from xtract.go. A Perl fallback is also available, and"
echo "will be used if necessary, so please disregard any errors below."
go build -o xtract."$osname" xtract.go
fi
echo ""
echo "Entrez Direct has been successfully downloaded and installed."
echo ""
prfx="In order to complete the configuration process, please execute the following:\n"
target=bash_profile
if ! grep "$target" "$HOME/.bashrc" >/dev/null 2>&1
then
if [ ! -f $HOME/.$target ] || grep 'bashrc' "$HOME/.$target" >/dev/null 2>&1
then
target=bashrc
else
if [ -n "$prfx" ]
then
echo -e "$prfx"
prfx=""
fi
echo " echo \"source ~/.bash_profile\" >>" "\$HOME/.bashrc"
fi
fi
if ! grep "PATH.*edirect" "$HOME/.$target" >/dev/null 2>&1
then
if [ -n "$prfx" ]
then
echo -e "$prfx"
prfx=""
fi
echo " echo \"export PATH=\\\$PATH:$DIR\" >>" "\$HOME/.$target"
fi
if [ -z "$prfx" ]
then
echo ""
echo "or manually edit the PATH variable assignment in your .bash_profile file."
echo ""
fi
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