sanger-pathogens/update_pipeline — pull request #27 by jm23 (2012-09-19 11:17:00+00:00)
Title: New SimpleLookup for species name and changed tags for optional parameters

I have added a SimpleLookup module to simply retrieve the scientific name of a species, where the taxon_id is provided (I was regularly getting connection errors with TaxonLookup with nightly updates - I have had none since using this). NOTE: this has a dependency on BioPerl module (Bio::DB::EUtilities).
There is also a default email set in the config files as the call to NCBI requires an email address.

As a result I have removed the species name gathering code from the Sample module in VRTrack.

I have given new tags to the optional parameters that we (Team 145) tend to use as I was getting in a knot trying to get sensible letters to use as tags! So taxon_id is -tax, no pending requests is -nop and so on. This makes our update script that calls update_pipeline.pl much easier to understand.....

I have been using these for a while, but give me a shout if there are any issues!

John