sequanix 0.2.0

Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows

Sequanix ######## Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.

.. image:: https://github.com/sequana/sequanix/actions/workflows/main.yml/badge.svg?branch=main :target: https://github.com/sequana/sequanix/actions/workflows/main.yml

.. image:: https://coveralls.io/repos/github/sequana/sequanix/badge.svg?branch=main :target: https://coveralls.io/github/sequana/sequanix?branch=main

.. image:: http://readthedocs.org/projects/sequana/badge/?version=main :target: https://sequana.readthedocs.io/en/main/sequanix.html :alt: Documentation Status

.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg :target: http://joss.theoj.org/papers/10.21105/joss.00352 :alt: JOSS (journal of open source software) DOI

:Python version: 3.8, 3.9, 3.10 :Documentation: On readthedocs <http://sequana.readthedocs.org/>_ :Issues: On github <https://github.com/sequana/sequana/issues>_ :How to cite: Citations are important for us to carry on developments.

For **Sequanix**: Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen,
Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer.
Sequanix: A Dynamic Graphical Interface for Snakemake Workflows 
Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034
Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)

Sequanix is a derivative of the Sequana project that is dedicated to the analyse of NGS data (sequencing data). We provide a set of NGS pipelines including quality control, variant calling, coverage, taxonomy, transcriptomics. Please see the Sequana documentation <http://sequana.readthedocs.org>_ for an up-to-date status and further information.

Notes

Fix OpenGL for mac Big Sur: https://stackoverflow.com/a/64021312/11988671

Installation ############

Please see the installation notes and installation steps on the https://sequana.readthedocs.io link.

In brief::

pip install sequanix

For developers, use::

git clone [e-mail]:sequana/sequanix.git
pip install -e .[testing]

Design choice #############

Uses PySide6 from v0.2.0. See e.g., https://www.pythonguis.com/faq/pyqt6-vs-pyside6/ from information on the switch to PySide6. In brief, the Qt project has recently adopted PySide as the official Qt for Python release which should ensure its viability going forward. When we migrate PyQt5 to PyQt6, we therefore decided to use PySide instead of PyQt.

Changelog

========= ==========================================================================
Version   Description
========= ==========================================================================
0.2.0     * add logo
          * remove pin on python3.7
          * switch from PyQt5 to PySide6
          * remove automatic creation of readtag in config. we let the pipelines
            handle it
0.1.0     * revamp Sequanix independently of Sequana
========= ==========================================================================