====== CRISPResso2 ======
CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

===== Information =====

  * Version: 2.3.2
  * Added: June, 2025
  * Link: https://github.com/pinellolab/CRISPResso2

===== Usage =====

See which versions are available:
<code>$ module avail crispresso2</code>

Load one version into your environment and run it:
<code>$ module load crispresso2/2.3.2
$ CRISPResso -h</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ module load python/3.10
$ sudo mkdir -p /export/apps/crispresso2/2.3.2
$ sudo chown aorth /export/apps/crispresso2/2.3.2
$ python -m venv /export/apps/crispresso2/2.3.2/.venv
$ source /export/apps/crispresso2/2.3.2/.venv/bin/activate
$ python -m pip install -U pip setuptools wheel
$ git clone https://github.com/pinellolab/CRISPResso2 -b v2.3.2
$ cd CRISPResso2
# Patch to use np.int64 instead of long, see: https://github.com/pinellolab/CRISPResso2/issues/535
$ sed -i 's/dtype=long/dtype=np.int64/' CRISPResso2/CRISPResso2Align.pyx
# See: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/crispresso2/meta.yaml
$ export CFLAGS="${CFLAGS} -O3 -Wno-implicit-function-declaration -Wno-int-conversion"
$ python -m pip install .
$ sudo chown -R root:root /export/apps/crispresso2/2.3.2</code>