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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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Issue with abricate databases #194

Open pedrofteixeira opened 1 year ago

pedrofteixeira commented 1 year ago

Hello Abricate team,

I installed abdicate through bioconda and when I run % abricate --list, instead of getting a list of databases I get this.

aminoglycoside 169 beta-lactamase 1305 colistin 1 fosfomycin 21 fusidicacid 2 macrolide 131 nitroimidazole 14 oxazolidinone 3 phenicol 36 quinolone 103 rifampicin 9 sulphonamide 49 tetracycline 104 trimethoprim 53 vancomycin 123 TOTAL 2123

Also, when I try choosing or updating a database (% abricate --db, % abricate-get_db) , these functions are not recognized.

Thank you for the assistance,

Pedro Teixeira

snayfach commented 1 year ago

I just installed through bioconda and am getting the proper list of databases. If you type which abricate is it pointing to the bioconda version you installed or a previously installed one?