pbiotools 2.0.0

"Miscellaneous bioinformatics and other supporting utilities for Python 3"

The pbiotools package provides miscellaneous bioinformatics and other supporting utilities for Python 3, including programs used for Ribo-seq periodicity estimation. It is required for the installation of Rp-Bp. It combines utilities and programs from the defunct pymisc-utils (see pyllars) and riboseq-utils.

Installation

To install the local VCS project in development mode, use the --editable or -e option, otherwise this flag can be ignored.

Pinned version of selected dependencies are listed in the requirements.txt file for reproducible installation.

Installation (virtual environment)

To install pbiotools and dependencies, first create a virtual environment:

python3 -m venv /path/to/virtual/environment

For information about Python virtual environments, see the venv documentation. To activate the new virtual environment and install pbiotools:

# Activate the new virtual environment.
source /path/to/virtual/environment/bin/activate

# If necessary, upgrade pip and wheel or additional packages (such as setuptools if installing in editable mode).
pip install --upgrade pip setuptools wheel

# Clone the git repository
git clone https://github.com/dieterich-lab/pbiotools.git
cd pbiotools

# The period is required, it is the local project path (pbiotools)
pip --verbose install -r requirements.txt [-e] . 2>&1 | tee install.log

Anaconda installation

The package can also be installed within an anaconda environment.

# Create the anaconda environment.
conda create -n my_new_environment python=3.6 anaconda

# Activate the new environment.
source activate my_new_environment

# Clone the git repository
git clone https://github.com/dieterich-lab/pbiotools.git
cd pbiotools

pip --verbose install -r requirements.txt [-e] . 2>&1 | tee install.log

Usage

There is currently limited documentation, see docs.

Uninstallation

To remove the pbiotools package:

pip uninstall pbiotools

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