Install with git

Installing DaisySuite

If you prefer to use Conda, you can find instructions in the Install with Conda chapter.

To use DaisySuite, the following dependencies need to be satisfied and globally available:

• bedtools
• biopython
• bwa
• clever-toolkit (Laser)
• gustaf
• mason2
• pandas
• pysam
• sak
• samtools
• scipy
• snakemake
• stellar
• yara

To install DaisySuite, run

git clone https://gitlab.com/eseiler/DaisySuite.git
cd DaisySuite
chmod +x DaisySuite*

For easy access, you might want to add the DaisySuite directory to your PATH variable, e.g.

export PATH=~/DaisySuite/:$PATH

Additional dependency for Laser

Laser uses bwa for structural variation analysis and requires the additional bwa perl script xa2multi.pl that is usually not installed with bwa, but is available in the bwa github.
xa2multi.pl needs to be present in the $PATH variable in order to use Laser, for example:

mkdir ~/bin
cd ~/bin
wget https://raw.githubusercontent.com/lh3/bwa/master/xa2multi.pl
export PATH=~/bin:$PATH

Setting DaisySuite up

You can automatically download and create all required data by running DaisySuite_setup <dir>. This will put the NCBI database and corresponding indices into the directory <dir>.
Alternatively, the requirements are explained in the Database requirements section.