README.md

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:

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