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bg7 / BG7

bacterial genome annotation system
bg7.ohnosequences.com
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no /proc/cpuinfo on MAC #32

Closed zachcp closed 5 years ago

zachcp commented 11 years ago

As a follow up to Issue 31, there is another Mac-specific error in the launch script. 

./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 
grep: /proc/cpuinfo: No such file or directory

To get around the error I can manually set the number of cores (line217) to: cores + "1" which works fine but any higher number of cores will crash the application because, apparently, threading is not supported on OSX .

best regards, zach cp

mscook commented 11 years ago

Hi,

This is not official, but I did something like this:

https://gist.github.com/4174156

(want to be able to set the number of CPU/threads when running in a shared environment)

Cheers

Mitch

mscook commented 11 years ago

Please note:

Changes on lines 55-56 relate to issue 22 (which has not been resolved).

Cheers

Mitch

eparejatobes commented 11 years ago

yeah we need to improve OS compatibility of the scripts