Installation

Containers

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

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

There is no latest tag, you need to specify the version tag. See ribotools/tags for valid values for <tag>.

Conda installation

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

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

or create an environment, called ribotools, containing the Ribotools package

conda create -n ribotools ribotools

Tip

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

Contributing to Ribotools

To install the local VCS project in development mode

# create a conda environment...
mamba env create -n ribotools
# ... activate...
mamba activate ribotools
# ... and install dependencies...
mamba install --only-deps ribotools
# ... clone the git repository and install the package
git clone https://github.com/eboileau/ribotools.git && cd ribotools
pip install --no-deps --editable . 2>&1 | tee install.log

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

mamba create -f environment.yml
# ... activate environment...
mamba activate ribotools
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 ribotools
# ... activate...
source ribotools/bin/activate
# ... and install the package
pip install ribotools

Required dependencies: Flexbar, Bowtie 2, STAR, Samtools, and FastQC. You also need a working R installation with additional packages.

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 conda environment

mamba env remove --name ribotools

or remove the package installed in another environment

# remove the ribotools package from myenv environment...
mamba remove -n myenv ribotools

To remove Ribotools if installed with pip

pip uninstall ribotools

If the package is installed in a dedicated python virtual environment, remove this environment.