https://github.com/bfssi-bioinformatics-lab/centreseq

Easily establish a core genome among bacterial strains
https://github.com/bfssi-bioinformatics-lab/centreseq

Last synced: over 1 year ago
JSON representation

Easily establish a core genome among bacterial strains

• Host: GitHub
• URL: https://github.com/bfssi-bioinformatics-lab/centreseq
• Owner: BFSSI-Bioinformatics-Lab
• License: mit
• Created: 2019-05-31T18:06:29.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2022-06-14T17:19:41.000Z (about 4 years ago)
• Last Synced: 2025-02-23T12:41:01.254Z (over 1 year ago)
• Language: Python
• Size: 456 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/centreseq/README.html)

[![Documentation Status](https://readthedocs.org/projects/centreseq/badge/?version=latest)](https://centreseq.readthedocs.io/en/latest/?badge=latest)

The most recent documentation can be found at the following URL: https://centreseq.readthedocs.io/en/latest/

### Quick installation in a Conda environment

Due to some strange Conda/Bioconda issues with both centreseq and Prokka, 

the installation process is convoluted to get everything working. The following incantation should work: 

```text

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

conda create -n centreseq python=3.7

conda activate centreseq

conda install centreseq -c bioconda

conda uninstall prokka

conda install -c conda-forge -c bioconda -c defaults prokka

conda install centreseq -c bioconda

```

### Developer notes/Known issues

- Version of mmseqs2 has been pinned at 9-d36de in meta.yaml due to 10-6d92c containing a bug which causes the functional test to 

hang indefinitely on some systems.

- Prokka's installation appears to be broken in some cases when just running `conda install prokka -c bioconda`, 

the solution is to downgrade Perl with `conda install perl=5.22.0`