Installing CRISPResso2 from source

[kclem]

To install CRISPResso2 from source (so you get the most recent updates):

1. Make sure you are in an environment with CRISPResso requirements (e.g. numpy, Flash, Trimmomatic, etc). If you don't have an environment, you can create a conda environment using conda create -n crispresso2_env -c bioconda crispresso2 and then activate it conda activate crispresso2_env

2. Download the source code from here:

wget https://github.com/pinellolab/CRISPResso2/archive/refs/heads/master.zip

2. Unzip the sourcecode:

unzip master.zip

3. Change into that directory

cd CRISPResso2-master/

4. Run setup.py

python setup.py install

Note that this will overwrite any CRISPResso installation that is currently in the environment.

You should be able to run CRISPResso --help to make sure CRISPResso is installed correctly.