Installation¶

Warning

CapCruncher is currently only availible for linux. MacOS support is planned for the future.

Setup¶

It is highly recommended to install CapCruncher in a conda environment. If you do not have conda installed, see the detailed conda installation section.

Dependencies¶

There are two main ways to obtain the dependencies required to run CapCruncher:

Install all dependencies using conda¶

Direct Installation¶

The easiest way to install these dependencies is to use conda. Run the following command to install CapCruncher and all dependencies:

mamba install -c bioconda capcruncher

Warning

The latest version of CapCruncher is not yet available on conda. Please install the latest version from PyPI using the command below.

Two-step installation using conda and pip¶

Alternatively, create a new conda environment and install CapCruncher using pip (currently the recommended method):

wget https://raw.githubusercontent.com/sims-lab/CapCruncher/master/environment.yml
conda env create -f environment.yml
conda activate cc

# Install CapCruncher using pip
pip install capcruncher
s
# Optional - highly recommended to install the optional dependencies
# Installs dependencies for:
# * plotting,
# * differential interaction analysis
# * speeding up the pipeline using experimental features (capcruncher-tools)
pip install capcruncher[full]

Install CapCruncher in a minimal conda environment and use singularity to run the pipeline¶

Note

Singularity must be installed on your system to use this method. See the pipeline guide for more information. The pipeline will only function correctly if using the --use-singularity option. This is because the pipeline uses singularity containers to run the pipeline steps. See the pipeline guide for more information.

Create a minimal conda environment and install CapCruncher using pip:

mamba create -n cc "python>=3.10"
conda activate cc
# Optional - highly recommended to install the optional dependencies
pip install capcruncher[stats,plotting,experimental]

Manual Installation (Not Recommended)¶

Install Dependencies¶

See the dependencies in the environment.yml and requirements.txt files. All dependencies can be installed using conda or pip.

Install CapCruncher from GitHub¶

Clone the repository and install CapCruncher using pip:

git clone https://github.com/sims-lab/CapCruncher.git
cd CapCruncher
pip install .

# Optional - highly recommended to install the optional dependencies
pip install .[stats,plotting,experimental]

Detailed Conda Installation Instructions¶

Download and install MambaForge from here for your system (You will typically need the x86_64 version for most Linux systems).

Download and run the installer for your system (only Linux is supported at the moment)¶

# Download the installer for your system
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh

# Allow the installer to be executed
chmod +x Mambaforge-Linux-x86_64.sh

# Run the installer
./Mambaforge-Linux-x86_64.sh

Follow the instructions to install MambaForge. It is advised to install MambaForge in a location with a reasonable amount of free space (>2GB) as it will be used to install all dependencies for CapCruncher.

Initialise MambaForge in your shell¶

conda init bash

Refresh your shell¶

source ~/.bashrc

Setup conda channels¶

conda config --set channel_priority strict
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Now the installation installation of CapCruncher can be completed using the instructions above.