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bg7 / BG7

bacterial genome annotation system
bg7.ohnosequences.com
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readlink error on macosx #31

Closed zachcp closed 3 years ago

zachcp commented 11 years ago

Hi BG7 Team,

In trying the BG7 platform I ran into a problem with your launcher script. I am running BG7 with the example data you provide as follows, but get an error in readlines:

/bin/bg7 -g escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta -c genetic_code.txt -p EHEC_ReferenceProteins_17_08_2012.fasta -r EHEC_Reference_RNAs.frn -G GenBankExternalData.xml -v
readlink: illegal option -- f
usage: readlink [-n] [file ...]

A quick google search points me to a this post which says that readlines -f isn't possible on MacOSX. They recommend a few alternatives, but I ended up doing a find/replace in bin/bg7 to use 'greadlines' instead of 'readlines.'

So BG7 won't work out of the gate for your Mac users.

thanks and looking forward to testing BG7, zach cp

eparejatobes commented 11 years ago

yep, OSX compat of the scripts is something that we didn't tested yet. We'll try to release a more compatible version