gbprocess-ngs 3.0.1

GBprocesS allows for the extraction of genomic inserts from NGS data for GBS experiments

Gbprocess

Description

GBprocesS allows for the extraction of genomic inserts from NGS data for GBS experiments. Preprocessing is performed in different stages that are part of a linear pipeline where the steps are performed in order. GBprocesS provides a flexible way to adjust the functionality to your needs, as the operations required and the execution order vary depending on the GBS protocol used.

Documentation

An extensive manual of the GBprocesS package can be found on Read the Docs including detailed explanations and illustrations.

Citation

If you use GBprocesS, please cite "Schaumont, D. (2020) GBprocesS: Genotyping-by-Sequencing Data Processing Toolkit [Online]. Available online at https://gitlab.com/dschaumont/GBprocesS"

Installation

GBprocesS is being developed and tested on Linux. Additionally, some dependencies are only developped on Linux.

Via Git

Currently, there are two supported ways to download GBprocesS from Git. The first and easiest way is to clone the git repository:

git clone [e-mail]:dschaumont/gbprocess.git

The second is to download an archive:

wget https://gitlab.com/dschaumont/GBprocesS/-/archive/2.0.2/GBprocesS-2.0.2.tar.gz
tar -xvf GBprocesS-2.0.2.tar.gz
mv GBprocesS-2.0.2 gbprocess

Afterwards, the package can be installed using the latest version of pip3::

cd gbprocess
pip3 install --user .

This will install GBprocesS in $HOME/.local/bin. If an already existing installation is present, add the --upgrade parameter to install a newer version.

To install at another location, a virtual environment can be used::

python3 -m venv .venv
source .venv/bin/activate
cd gbprocess
pip install .

A new folder .venv will be created in the current working directory, and GBprocesS will be installed at that location. Please note that you will need to activate the virtual environment again when you start a new session using the source command above.

After the installation, test if the program is correctly installed by using::

gbprocess --help