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 new environment...
mamba create -n rpbp
# ... activate...
mamba activate rpbp
# ... and install dependencies...
mamba install --only-deps rpbp
# ... clone the git repository and install the package
git clone https://github.com/dieterich-lab/rp-bp.git && cd rp-bp
pip install --no-deps --editable . 2>&1 | tee install.log

Alternatively, clone the git repository and install from the yaml spec file

mamba env create -f environment.yml
# ... activate environment...
mamba activate rpbp
pip install --no-deps --editable . 2>&1 | tee install.log

Finally, install test dependencies.

PyPI installation

To install the package from PyPI

# create a virtual environment...
python3 -m venv rpbp
# ... activate ...
source rpbp/bin/activate
# ... and install the package
pip install rpbp

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

Warning

A PyPI installation only installs the python package. You need to install required dependencies separately. Executables or binaries must be in your $PATH.

Uninstallation

Remove the environment

mamba env remove --name rpbp

or remove the package installed in another environment

# remove the rpbp package from myenv environment...
mamba 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, remove this environment.