Installation of required software#

It is recommended to run GPSW on a Linux-based system (e.g. Ubuntu).

Make sure you have Conda installed.

Installation of the latest version via Conda#

The easiest wasy to install GPSW is via Conda, which will handle all dependencies automatically.:

$ conda install -c bioconda gpsw
Installation of older versions

To install versions older than “0.7.0” use the following command:

$ conda create -n gpsw=0.6.3 bioconda::gpsw pandas=2.2.3  pygments=2.19.1 conda=24.7.1

Otherwise, run:

$ conda create -n gpsw=VERSION

All available releases can be found on the GitHub releases page.

Installation of development version#

First, create a yaml file with the environment configuration, e.g. gpsw.yaml:

name: gpsw
channels:
   - conda-forge
   - bioconda
   - defaults
dependencies:
   - python=3.12
   - pygithub=2.6.1
   - pydot=3.0.4
   - apptainer=1.4.0 # [linux]
   - snakemake-minimal=8.25.5
   - numpy=2.2.6
   - pandas=2.2.3
   - pygments
   - conda=24.7.1

Note

Apptainer will not be installed on non-Linux systems, as it is not available for MacOS.

Then, create the environment using the yaml:

$ conda env create -f gpsw.yaml

Important

If you want to use Apptainer, it is essential to install Snakemake 8.25.5, as other versions might not work with the pre-build image.

To install GPSW:

$ cd /path/to/clone/gpsw
$ git clone https://github.com/niekwit/gps-orfeome.git
$ cd gps-orfeome
$ pip install -e .

At a later point, GPSW can be updated:

$ git pull

Installation of Snakemake plugins#

Snakemake plugins are required for the workflow to run correctly in certain environments. Please follow the instructions here to install the required plugins.