Installation
Install from GitHub
Download the zip file of your preferred release from GitHub and unzip it. Then go into the unzipped folder. You can get the link to the zip file of the newest version from the GitHub release page.
wget https://github.com/ZarnackGroup/racoon_clip/archive/refs/tags/[version].zip
unzip [version].zip
cd racoon_clip-[version]
It is recommended to install racoon_clip in a fresh conda/mamba environment. You could for example install the prerequisites with conda:
conda create -n racoon_clip \
--override-channels -c conda-forge \
mamba=1 \
'python_abi=*=*cp*' \
python=3.9.0 \
pip=25.0
conda activate racoon_clip
or if you already have mamba installed:
mamba create -n racoon_clip python=3.9.0 pip=25.0
mamba activate racoon_clip
Then install racoon with pip.
pip install -e .
# Inside a conda environment, do the following to avoid pip clashes:
# Find your anaconda directory and the folder of the environment.
# (It should be somewhere like /anaconda/envs/racoon_clip/.)
/anaconda/envs/racoon_clip/bin/pip install -e .
Check Installation with Tests
You can now check the installation by running the help option and then quickstart your analysis.
racoon_clip -h
Furthermore, racoon_clip provides built-in test commands to verify your installation:
Light Test (Quick verification):
racoon_clip test --light
This runs a quick test doing basic functionality checks
Full Test (Comprehensive verification):
racoon_clip test
This runs the complete test suite including:
All tests from the light test
Full workflow execution tests with example data
Use Docker Image
If your system has Docker or Apptainer installed, you can also use the racoon_clip Docker Image. Slurm job scheduling of the racoon_clip jobs is not supported by the Docker image. At the moment, usage of SingularityCE containers is also not supported.
docker pull melinak/racoon_clip:latest
or
apptainer pull racoon_clip.sif docker://melinak/racoon_clip:latest
We also provide a quick explanation on how to use racoon_clip inside a container.