instructions for indexing database files?

[kapsakcj]

Hi, I was hoping to test out ShigaPass and when I went to run the script, it threw an error that no index files were found.

### ipaH checkpoint ###
BLAST Database error: No alias or index file found for nucleotide database [SCRIPT/ShigaPass_DataBases//IPAH/ipaH_150-mers.fasta] in search path [/home/curtis_kapsak/github/ShigaPass::]

Could you provide instructions on how to index the databases? I assume I can use the makeblastdb command, but wasn't sure what options should be used, if any.

It would be helpful to have these instructions on the main README.md.

Thank you

[kapsakcj]

I ended up running makeblastdb -dbtype nucl <fasta> on all the fasta files included w/ ShigaPass, and ShigaPass ran successfully afterwards

[kapsakcj]

Apologies, I did not see the command line option -u for indexing the databases, though it seems that I got the command correct:

ShigaPass/SCRIPT/ShigaPass.sh

Line 112 in 1f72e53

for database in ${DBPATHWAY}/*/*.fasta; do makeblastdb -dbtype nucl -in ${database}; done

Maybe it would be worth highlighting on the README.md here, so that users like myself do not miss it! https://github.com/imanyass/ShigaPass#installation