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#60 make AmiGO better for non-GO ontology-only installs

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Seth Carbon
AmiGO 1.8 (12)
3
2010-10-27
2010-10-27
Seth Carbon
No

This is largely taken from an email thread from a group installing AmiGO for non-GO ontology browsing.

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- config.json was not found in amigo directory, then install.pl stopped improperly (I need to type touch config.json to solve this issue)
- since I did not install CVS, make_dblinks.pl script did not create db_info.pl until I run it with -n argument

When I found AMIGO_TERM_REGEXP option in config.pl, I have solved the input error "Term acc could not be found!".
Since gene product is not interesting for our ontology, I have set AMIGO_SHOW_GP_OPTIONS to 0, but I still had these issues:
- make_misc_key.pl create spec_keys.pl (FrT;@1|%0|) but not spec_ncbi_map.pl and spp_db_map.pl (I need to type copy spec_keys.pl spec_ncbi_map.pl and copy spec_keys.pl spp_db_map.pl to create them)
- cache system was not correct: cache files in afs_gp_cont_files directory only contains {}, then I had "something went south in the conversion" error. I have modified AmiGO/Worker/GeneProductCount.pm line 54 to solve this ("if( ! defined $cache ){" instead of "if( ! defined $cache || $self->empty_hash_p($cache) ){")

Discussion

  • Seth Carbon
    Seth Carbon
    2010-10-27

    I should be able to get most of this in easily for the first bit of 1.9.