Installation

CRISPResso can be installed using the conda package manager Bioconda, or it can be run using the Docker containerization system.

Bioconda

To install CRISPResso using Bioconda, download and install Anaconda Python, following the instructions at: https://docs.anaconda.com/free/anaconda/install/.

Open a terminal and type:

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

To install CRISPResso into the current conda environment, type:

conda install crispresso2

Alternatively, to create a new environment named crispresso2_env with CRISPResso, type:

conda create -n crispresso2_env -c bioconda crispresso2

Activate your conda environment:

conda activate crispresso2_env

Verify that CRISPResso is installed using the command:

CRISPResso -h

Bioconda for Apple Silicon

If you would like to install CRISPResso using bioconda on a Mac with Apple silicon (aren't sure?), then there is a slight change you need to make. First, ensure that you have Rosetta installed. Next, you must tell bioconda to install the Intel versions of the packages. If you would like to do this system wide, which we recommend, run the command:

conda config --add subdirs osx-64

Then you can proceed with the installation instructions above.

If you would like to use the Intel versions in a single environment, then run:

CONDA_SUBDIR=osx-64 conda create -n crispresso2_env -c bioconda crispresso2

If you choose to use the CONDA_SUBDIR=osx-64 method, note that if you install additional packages into the environment you will need to add the CONDA_SUBDIR=osx-64 to the beginning of each command. Alternatively, you could set this environment variable in your shell, but we recommend to use the conda config --add subdirs osx-64 method because it is less error prone.

Docker

CRISPResso can be used via the Docker containerization system. This system allows CRISPResso to run on your system without configuring and installing additional packages. To run CRISPResso, first download and install docker: https://docs.docker.com/engine/installation/.

Next, Docker must be configured to access your hard drive and to run with sufficient memory. These parameters can be found in the Docker settings menu. To allow Docker to access your hard drive, select 'Shared Drives' and make sure your drive name is selected. To adjust the memory allocation, select the 'Advanced' tab and allocate at least 4G of memory.

To run CRISPResso, make sure Docker is running, then open a command prompt (Mac) or Powershell (Windows). Change directories to the location where your data is, and run the following command:

docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPResso -h

The first time you run this command, it will download the Docker image. The -v parameter mounts the current directory to be accessible by CRISPResso, and the -w parameter sets the CRISPResso working directory. As long as you are running the command from the directory containing your data, you should not change the Docker -v or -w parameters.

Additional parameters for CRISPResso as described below can be added to this command. For example,

docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPResso -r1 sample.fastq.gz -a ATTAACCAAG