tripal / tripal_analysis_unigene

DEPRECATED. This module is no longer needed for Tripal v3. Only major bug fixes will be considered for Tripal v2 sites that still use it. But, in summary, This module extends the Tripal v2 Analysis Module and provides visualization of Unigenes derived from ESTs.

DEPRECATED

This module is no longer needed for Tripal v3 or later.

Summary

In summary, This module extends the Tripal v2 Analysis Module and provides visualization of Unigenes derived from ESTs.

Conversion of Tripal v2 Unigene Analyses to Tripal v3

First, be sure you have the most recent run updatedb for this module so you have the analysis_type set • define a unigene bundle with that cvterm config • run alchemist “automatic” with the vanilla analysis as the soruce and your new, unigene bundle as aathe destination (edited) the first step is necessary because as that issue points out, it uses some random property (analysis_unigene_name?) to determine if its a unigene (edited) alternatively you could create a Tripal 3 collection of all the analyses you want to convert. Alchemist supports collections.

tripal_analysis_unigene's Issues

unigene analyses do not set the analysis_type prop

Analysis unigene looks to see if the analysis_unigene_name prop is set to determine if an analysis is an analysis_unigene type (or it looks at the node type). For Tripal 3 we can create a unigene bundle type, but need to specify a property with a fixed value to determine the type.

The best fix (i think) is to update the module to set the analysis_type prop to tripal_analysis_unigene, and to write an update script that will set insert the prop in chado if it isnt set. I plan on submitting a PR for this issue soon.

for more info see
statonlab/hardwoods_site#55