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chado gmod_bulk_load_gff3.pl error

When use chado gmod_bulk_load_gff3.pl, there is an error:

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/share/perl/5.26.1/Bio/GMOD/DB/Adapter.pm line 498.
Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl line 13.
BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl line 13.

I try to switch to an earlier version perl, but it not ok?

Is there another way to run it

gff3 chado load
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updated by Ram Ram • written by 82101202089 • 82101202089

1 answer

There are several options here:

  • go back to an earlier perl version, use of defined (@array) was deprecated in 5.16 and then turned into a compile error somewhere in 5.22, use e.g. perl 5.20 and you will be ok
  • provide a bug report on the gmod chado mailing list or on their bug tracker in github: https://github.com/GMOD/Chado
  • try the github version: https://github.com/GMOD/Chado or one of its forks, maybe it is already fixed there
  • fix the error locally as advised by the error message. Edit the file /usr/local/bin/gmod_bulk_load_gff3.pl in line 13 and delete defined. Hopefully, this was the only error. Check syntax by running perl -c /usr/local/bin/gmod_bulk_load_gff3.pl, fix any errors, rinse and repeat.
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written by Michael Dondrup Michael Dondrup

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