Installation

Software dependencies

It is recommended to use a conda environment to handle dependencies. To do so, CrassUS comes with the file conda-linux-64.lock, enumerating the software needed to run the pipeline. To get a working conda environment with these software installed:

$ git clone https://github.com/dcarrillox/CrassUS.git
$ cd CrassUS

# Note the long notation --file flag; -f will not work.
$ conda create -n crassus --file=conda-linux-64.lock

# Activate it - use the name you gave above, if it is different
$ conda activate crassus

# The (crassus) prefix shows we have activated it
# Check the snakemake version
(crassus) $ snakemake --version
6.6.1