"Miscellaneous bioinformatics and other supporting utilities for Python 3"
Project description
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.
Project details
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