Basic installation instructions for the tools. We advise you use Ubuntu 16.04 or later.

We are going to put most executables inside the directory "$HOME/.local/bin" that should already be in your PATH. If it isn't, add it.

Make sure both .local/bin and .local/lib exist:

mkdir -p $HOME/.local/bin $HOME/.local/lib

There might be dependencies you haven't installed yet. It should be clear from the error output what library you have to
install to make it work. These will all be available in the Ubuntu repositories.

A good start is to have the build-essential package installed beforehand:

sudo apt-get install build-essential

1. Bedtools

sudo apt-get install bedtools

The version of this doesn't matter, so we can use the package in the repositories.

Or from sources, if you prefer.

2. BWA

wget https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2
tar xvfj bwa-0.7.15.tar.bz2
cd bwa-0.7.15
make
cp bwa ~/.local/bin

3. samtools

wget https://github.com/samtools/samtools/releases/download/1.4.1/samtools-1.4.1.tar.bz2
tar xvfj samtools-1.4.1.tar.bz2
cd samtools-1.4.1
./configure --prefix=$HOME/.local/bin
make all all-htslib
make install install-htslib

4. GATK

Go here:

https://software.broadinstitute.org/gatk/download/

Follow instructions to download version 3.7, then do:

tar xvfj GenomeAnalysisTK-3.7.tar.bz2
cp GenomeAnalysisTK.jar $HOME/.local/lib

5. Poretools

First install pip, either with apt-get or (as we advise) following these instructions:

https://pip.pypa.io/en/stable/installing/

Then simply run:

pip install poretools --user

6. Picard

wget https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar
cp picard.java $HOME/.local/lib

7. Nanopolish

git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make
cp nanopolish $HOME/.local/bin
cp scripts/* $HOME/.local/bin