Install with Conda

Installing DaisySuite

We recommend the usage of Conda to install DaisySuite.
If you prefer to not use Conda, you can find instructions in the Install with git chapter.

To install Conda under Linux 64bit, run

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

and follow the instructions.
Please visit the Miniconda homepage for further information.

Next, add the bioconda channel to your conda installation.

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Once Conda is available, DaisySuite can be easily installed via

conda install daisysuite

Note that older or newer versions of already on your system existing tools, e.g. bwa, will be installed according to the specified requirements for DaisySuite in the Conda package.
To install DaisySuite in a new environment and thereby not altering any of your existing installations, use

conda create -n daisysuite_env daisysuite

where -n daisysuite_env specifies the environment name and can be chosen freely.
Use source activate daisysuite_env to activate your new environment and source deactivate to exit the environment.

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. Yara needs up to 1 TB of temporary disk space to create its index. Currently, the setup script will fail if one of the steps fails. In this case, consider running the individual steps one by one (see the Database creation section).