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|
#!/bin/bash
# This setup script installs gubbins and dependencies on Ubuntu 14.04 x86_64.
# In particular, we set things up in the users' home directory in ~/.local (as
# per the XDG spec). We also add ~/.local/bin to PATH and ~/.local/lib to
# LD_LIBRARY_PATH.
#
# If you'd prefer to install this system wide, have a look at the documentation
# at https://github.com/AidanDelaney/gubbins
#
# Contact Aidan Delaney <aidan@ontologyengineering.org> for issues with this
# script.
#
py_pkgs=( "biopython" "dendropy" )
deb_urls=( "http://uk.archive.ubuntu.com/ubuntu/pool/universe/r/raxml/raxml_7.2.8-2_amd64.deb" "https://launchpad.net/~ap13/+archive/ubuntu/gubbins/+files/gubbins_1.3.3~trusty1_amd64.deb" )
function check_platform {
# Ubuntu 14.04
echo -n "Checking Platform "
source /etc/lsb-release
case $DISTRIB_DESCRIPTION in
"Ubuntu 14.04")
echo "pass"
;;
*)
echo "This setup script has only been tested on Ubuntu 14.04 but will continue with the installation process."
;;
esac
case "$(uname -m)" in
"x86_64")
echo "pass"
;;
*)
echo "This setup script only works on Ubuntu x86_64"
exit
;;
esac
}
function check_dependencies {
# Python 2.7
echo -n "Checking Python 2.7 "
case "$(python --version 2>&1)" in
*" 2.7"*)
echo "pass"
;;
*)
echo "Wrong Python version! Please ensure you are using Python 2.7"
exit 1
;;
esac
echo -n "Checking Python development headers "
# ensure python-dev is installed
dpkg -s python-dev > /dev/null 2>&1
if [ $? -eq 0 ] ; then
echo "pass"
else
echo "No Python.h on this system. Please ensure python-dev is installed."
exit 1
fi
# wget
echo -n "Checking wget "
if hash wget 2>/dev/null; then
echo "pass"
else
echo "No wget found"
exit 1
fi
}
function install {
# install Python setuptools
wget https://bootstrap.pypa.io/ez_setup.py -O - | python - --user
for pkg in ${py_pkgs[@]}
do
${HOME}/.local/bin/easy_install -U --user $pkg
done
for deb in ${deb_urls[@]}
do
wget $deb
done
# extract all debs to a subfolder
mkdir expanded
# expand each deb
for deb in *.deb
do
dpkg -x ${deb} expanded/.
done
# copy binaries to ~/.local/bin
cp expanded/usr/bin/* ~/.local/bin
cp expanded/usr/lib/x86_64-linux-gnu/libgubbins.* ~/.local/lib
cp -R expanded/usr/lib/python2.7/ ~/.local/lib
rm -rf expanded
}
function verify_path {
# tell the user session to pick up the installed tools
cat >> ~/.bashrc <<EOF
LD_LIBRARY_PATH=~/.local/lib${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH:-}
export LD_LIBRARY_PATH
PATH=~/.local/bin${PATH:+:}${PATH:-}
export PATH
EOF
echo "" >> ~/.bashrc
echo "run 'source ~/.bashrc' to ensure you can find gubbins"
}
check_platform
check_dependencies
install
verify_path
|
