kristyhoran / coreuscan Goto Github PK
View Code? Open in Web Editor NEWA tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
When you pip install it is coreuscan
- no .py
extension.
pip3 install git+https://github.com/kristyhoran/coreuscan.git#egg=coreuscan
Anything after the hash is a comment
Do you need to quote it?
Add installation and workflow
I tried running coreuscan.py -d -s listeria -st cg -db Pasteur -o path_for_scheme exactly as listed in the documentation and got the following error:
======================================================>
Searching for listeria
======================================================>
The cache does not yet exist. Please wait.....
Requesting data from Enterobase @ enterobase.warwick.ac.uk
404 Client Error: Not Found for url: http://enterobase.warwick.ac.uk/schemes/Salmonella.cgMLSTv4/
Any assistance you could provide to correct this would be greatly appreciated.
Hello,
When I try and run coreuscan --download --database enterobase -s senterica -st cg
I get the following error message:
404 Client Error: Not Found for url: http://enterobase.warwick.ac.uk/schemes/Salmonella.cgMLSTv4/
It looks like Enterobase doesn't have a version 4, only a version 2. Is there a way to give coreuscan
the complete path?
Thanks!
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