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).