Installation notes for Ubuntu
This page has detailed installation instructions that work using a clean install of Ubuntu 14.04 desktop edition. It avoids using root wherever possible, to show how to install without root permission.
Install core packages as root
You will need some packages installed on your system. The commands to run are:
sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu $(lsb_release -sc) universe" sudo apt-get update sudo apt-get install python3-pip zlib1g-dev libncurses5-dev libncursesw5-dev
These are the only dependencies that you will need root access to install. However, if you do have root, then a few things described below become easier:
- You don't need to make the changes below to use pip3 with the
- MUMmer and samtools can be installed with:
sudo apt-get install mummer samtools
From now on, we assume that you do not have root permission.
Setup user directory for dependencies
We'll add software required by IVA to a
bin/ directory in your home, so it needs to be made if
it doesn't already exist.
We will tell
pip3 to install to your home directory with the
This makes it install scripts to the directory
$PATH environment variable needs updating so that the dependencies and
scripts installed by
pip3 get found.
You may also want to add this to your
Install the dependencies
cd $HOME/bin wget http://sun.aei.polsl.pl/kmc/download/kmc wget http://sun.aei.polsl.pl/kmc/download/kmc_dump chmod 755 kmc kmc_dump
cd $HOME/bin wget http://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz tar -zxf MUMmer3.23.tar.gz cd MUMmer3.23 make cd .. for x in `find MUMmer3.23/ -maxdepth 1 -executable -type f`; do cp -s $x . ; done
cd $HOME/bin wget http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2 tar -xjf samtools-1.0.tar.bz2 cd samtools-1.0/ make cd .. cp -s samtools-1.0/samtools .
cd $HOME/bin wget http://downloads.sourceforge.net/project/smalt/smalt-0.7.6-bin.tar.gz tar -zxf smalt-0.7.6-bin.tar.gz cp -s smalt-0.7.6-bin/smalt_x86_64 smalt
pip3 install --user iva