Installation

The following steps are required to install pycrispr:

Installation Conda/Mamba (Mamba is highly recommended)

Installation of snakemake

Installation of pycrispr

1. Conda/Mamba installation

pycrispr requires the snakemake workflow management software, it highly recommended to install the mamba package manager first:

$ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" | bash

Note

Although highly recommended, using Conda/Mamba is not an absolute requirement. Using the pycrispr flags -c/–noconda, the Conda/Mamba requirement can be bypassed. However, it is then up to the user to install all the software and make sure they are set as environment variables.

2. Installation of snakemake

Next snakemake can be installed with the following commands:

$ mamba activate base
$ mamba create -c conda-forge -c bioconda -n snakemake snakemake

This will create a new virtual environment named snakemake.

3. Installation of pycrispr

Latest development version

From the snakemake virtual environment, run the following commands to install the latest development version of pycrispr:

$  mamba activate snakemake
$  cd /path/of/choice
$  git clone https://github.com/niekwit/pycrispr.git
$  cd pycrispr
$  pip install .

To update pycrispr to the latest version run:

$  cd /path/of/pycrispr
$  git pull
$  pip install --upgrade .

Installation of stable version via Python Packaging Index (PyPi)

$  pip install pycrispr

OPTIONAL: installation of BAGEL2

Besides MAGeCK, pycrispr can also use BAGEL2 to perform statistics. However, this would need to be installed by the user itself, as BAGEL2 is not available in the (Bio)Conda repositories:

$ cd path/to/clone/bagel2dir
$ git clone https://github.com/hart-lab/bagel.git

The BAGEL2 path can then be set in experiment.yaml (stats > bagel2_dir).