Installation

Containers

To use a container (Docker or Singularity) with Rp-Bp pre-installed, simply pull, and you’re done!

# docker or...
docker pull quay.io/biocontainers/rpbp:<tag>
# ...singularity
singularity pull rpbp.sif docker://quay.io/biocontainers/rpbp:<tag>

There is no latest tag, you need to specify the version tag. See rpbp/tags for valid values for <tag>. Check the Tutorials on how to use the containers.

Conda installation

If required, set up the conda channels as described here, and install with

# preferably install in some conda environment...
conda install rpbp

or create an environment, called rpbp, containing the Rp-Bp package

conda create -n rpbp rpbp

Tip

Mamba can be used as a drop-in replacement, you can swap almost all commands between conda and mamba.

Contributing to Rp-Bp

To install the local VCS project in development mode

# create a conda environment...
conda create -n rpbp_dev
# ...activate it...
conda activate rpbp_dev
# ... and only install dependencies (rpbp_dev is now activated)
conda install --only-deps rpbp
# clone the git repository
git clone https://github.com/dieterich-lab/rp-bp.git && cd rp-bp
# install
pip --verbose install --no-deps -e . 2>&1 | tee install.log

PyPI installation

We do not recommend to install Rp-Bp directly from PyPI. However, if you already have the required dependencies installed on your system, to install

# create a virtual environment...
python3 -m venv rpbp_pypi
# ... activate it ...
source rpbp_pypi/bin/activate
# ... and install Rp-Bp (rpbp_pypi is now activated)
pip install rpbp

Required dependencies: Flexbar, Bowtie 2, STAR, Samtools.

Warning

Conda installation or containers include all dependencies. With a PyPI installation, you need to install required dependencies. Executables or binaries must be in your $PATH.

Uninstallation

Remove the conda environment

conda env remove --name rpbp

or remove the package installed in another environment

# remove the rpbp package from myenv environment...
conda remove -n myenv rpbp

To remove Rp-Bp if installed with pip

pip uninstall rpbp

If the package is installed in a dedicated python virtual environment, this environment can also be removed.