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Installation notes for Ubuntu

martinghunt edited this page Oct 21, 2015 · 7 revisions

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 --user option
  • 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.

mkdir $HOME/bin

We will tell pip3 to install to your home directory with the --user flag. This makes it install scripts to the directory $HOME/.local/bin/. The $PATH environment variable needs updating so that the dependencies and scripts installed by pip3 get found.

export PATH=$PATH:$HOME/bin/:$HOME/.local/bin/

You may also want to add this to your ~/.bashrc file.

Install the dependencies

KMC

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

MUMmer

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

Samtools

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 .

SMALT

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

Install IVA

pip3 install --user iva
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