hoelzer
commented
3 years ago As far as I have seen, BioPython and blast are the only dependencies, right? We have those covered already, so it should run more or less out of the box.
We'd have to look at the hardcoded paths (
config.pyfor example) though.
Yeah, it was not the plan to directly integrate this in RIBAP (now) but more to have this scripts also in a repository for the current Chlamydia 33er genome comparison publication. In this context I asked @MarieLataretu to simply upload the scripts as helpers to the RIBAP repo because we anyway cite it in the manuscript. :)
But of course, could be also a future extension of the RIBAP pipeline
- after prokka step, check for a gene that is common in all genomes (or user defined)
- rearrange for this gene
- continue
As far as I have seen, BioPython and blast are the only dependencies, right? We have those covered already, so it should run more or less out of the box.
We'd have to look at the hardcoded paths (
config.pyfor example) though.