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