tripal_feature_load_gff3 v gmod_bulk_load_gff3 and load performance

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tripal_feature_load_gff3 v gmod_bulk_load_gff3 and load performance

Cook, Malcolm

I notice that some gmod_bulk_load_gff3 are not present in its apparent replacement, tripal_feature_load_gff3, and wonder why.
In particular the gmod_bulk_load_gff3 --drop_indexes and--skip_vacuum options seems no longer present in tripal_feature_load.

Also, can anyone confirm that:

        --notransact is replaced by use_transaction

I am asking these questions in pursuit of helping a colleague (hi Sofia) sleuth options for speeding up a large GFF3 load under tripal.

In addition to normal pg tuning, advice I have seen before with Drupal includes:
        Split up a large GFF into multiple files
        Don't use transactions
        Drop indices and add them back post-load

Anyone have additions of amendments to these suggestions in the context of Tripal?  I.E, which if any of these strategies still works, or would still work if modified appropriately.

Finally, I see a web interface in Tripal to invoking tripal_feature_load_gff3 but see no command line equivalent.  Can someone explain why, or am I missing something?  Must GFF be loaded via web interface now?



Malcolm Cook
Computational Biology
Stowers Institute for Medical Research
1000 E 50th Street
Kanas City, MO 64110
(816) 926-4449
[hidden email]

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