I may be being stupid, but working through the tutorial, I have no idea where isolates_config.cfg comes from nor what it contains, and it is not installed by default from bioconda.
Could it be made more clear where this config file comes from and what it contains?
Hi and thanks for reporting this.
I guess you’re referring to the High-resolution phylogeny of 135 Staphylococcus aureus isolate genomes example.
The phylophlan_write_config_file command was probably not in a convenient place (it was at the end of Step 3., after the PhyloPhlAn command). I’ve now changed and put it under the new Step. 3 section so it should be more clear and easy to follow the tutorial.
Many thanks for your help on improving our tutorials,
Francesco
Yes, thank you Francesco, that is now much clearer!