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install.ubuntu.sh
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install.ubuntu.sh
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#!/bin/sh
#
# This script is designed install pre-requisites for PrimerSeq on linux
# (Debian based distros with apt-get). The following is assumed when you run
# this script:
#
# You have root access
# The default python version is 2.7.X
tty -s; if [ $? -ne 0 ]; then konsole -e "su root - -c $0"; exit; fi
EXPECTED_ARGS=0
E_BADARGS=65
if [ $? -ne $EXPECTED_ARGS ]
then
echo "This script is designed to install pre-requisites for PrimerSeq on linux (Debian based distros with apt-get). It is assumed you have the following:\n* root access\n* Default Python version is 2.7"
exit $E_BADARGS
fi
# build primer3 version 2.3.5 from source
wget "https://sourceforge.net/projects/primer3/files/primer3/2.3.5/primer3-2.3.5.tar.gz/download" -O primer3.tgz
tar xvzf primer3.tgz
mv primer3-2.3.5 primer3
cd primer3/src
make all
cd ../..
# Get dependencies of pip
sudo apt-get install python-setuptools
sudo apt-get install python-pip
# install python-dev for numpy installation
sudo apt-get install python-dev
# possible dependencies for matplotlib
sudo apt-get install libtiff
sudo apt-get install libpng
# install matplotlib through apt-get
sudo apt-get install matplotlib
# install python dependencies
sudo pip install numpy
sudo pip install pygr
sudo pip install networkx
### Code for installing on old versions of ubuntu ###
# add wxwidgets to sources list
# sudo echo "deb http://apt.wxwidgets.org/ `lsb_release -a | grep Codename | cut -f2`-wx main
# deb-src http://apt.wxwidgets.org/ `lsb_release -a | grep Codename | cut -f2`-wx main" > /etc/apt/sources.list.d/wxwidgets.list
# update so wxwidgets repo is found with apt-get
# sudo apt-get update
# install wxPython
# sudo apt-get install python-wxgtk2.8 python-wxtools wx2.8-i18n libwxgtk2.8-dev libgtk2.0-dev
# install wxPython for new ubuntu versions
sudo apt-get install python-wxgtk2.8