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|
#!/bin/bash -norc
PERL=perl
case "`uname -s`" in
Darwin )
PERL=/usr/bin/perl
;;
esac
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"
if ! "${PERL}" -Iaux/lib/perl5 -MMozilla::CA -e '1;' 2>/dev/null
then
gzip -cd Mozilla-CA.tar.gz | tar xvf -
fi
mkdir -p _cpan/CPAN
echo '1;' >> _cpan/CPAN/MyConfig.pm
if ! "${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
elif grep '^SSLeay\.xs:.*[Ee]rror:' setup-deps.log >/dev/null
then
cat <<EOF
Unable to build Net::SSLeay. Please install either a prebuilt version
of this module or OpenSSL development files to build it against.
EOF
fi
fi
rm -rf _cpan
osname=`uname -s`
cputype=`uname -m`
case "$osname-$cputype" in
Linux-x86_64 ) platform=Linux ;;
Darwin-x86_64 ) platform=Darwin ;;
Darwin-*arm* ) platform=Darwin ;;
CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;;
Linux-*arm* ) platform=ARM ;;
* ) platform=UNSUPPORTED ;;
esac
if [ -n "$platform" ]
then
./nquire -dwn ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract."$platform".gz
gunzip -f xtract."$platform".gz
fi
if [ -f xtract."$platform" ]
then
chmod +x xtract."$platform"
else
echo "Unable to download xtract executable."
fi
if [ -n "$platform" ]
then
./nquire -dwn ftp.ncbi.nlm.nih.gov /entrez/entrezdirect transmute."$platform".gz
gunzip -f transmute."$platform".gz
fi
if [ -f transmute."$platform" ]
then
chmod +x transmute."$platform"
else
echo "Unable to download transmute executable."
fi
if [ -n "$platform" ]
then
./nquire -dwn ftp.ncbi.nlm.nih.gov /entrez/entrezdirect rchive."$platform".gz
gunzip -f rchive."$platform".gz
fi
if [ -f rchive."$platform" ]
then
chmod +x rchive."$platform"
else
echo "Unable to download rchive executable."
fi
echo ""
echo "Entrez Direct has been successfully downloaded and installed."
echo ""
prfx="In order to complete the configuration process, please execute the following:\n"
advice=`mktemp`
target=bash_profile
if ! grep "$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" | tee $advice
fi
fi
if ! grep "PATH.*edirect" "$HOME/.$target" >/dev/null 2>&1
then
if [ -n "$prfx" ]
then
echo -e "$prfx"
prfx=""
fi
echo " echo \"export PATH=\\\${PATH}:$DIR\" >>" "\$HOME/.$target" \
| tee $advice
fi
if [ -z "$prfx" ]
then
echo ""
echo "or manually edit the PATH variable assignment in your .bash_profile file."
echo ""
echo "Would you like to do that automatically now? [y/N]"
read response
case "$response" in
[Yy]* ) . $advice; echo "OK, done." ;;
[Nn]* | '' ) echo "Holding off, then." ;;
* ) echo "Conservatively taking that as a no." ;;
esac
fi
rm $advice
|
