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elsiklab / jbrowse_elasticsearch

A JBrowse plugin for generating an elasticsearch database and an express.js adaptor for the Names API
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[Question] About indexing #6

Closed hsiaoyi0504 closed 6 years ago

hsiaoyi0504 commented 6 years ago

Hi, I am new to jbrowse and this plugin. I just get confused how to use this plugin. In Jbrowse document mentioned, it needs to run generate_names.pl to create index. However, I am not sure if I need to do that at this case, or I just need to use prepare-refseqs.pl, flatfile-to-json.pl, and generate_elastic_search.pl. Can someone help me this ?

cmdcolin commented 6 years ago

Essentially you can do both generate-names and generate-elastic-search

The plugin here makes a custom menu item for searching and should supplant most of the functionality of generate-names but the generate-names is still useful to run. For example the box that shows your location doubles as a search box that generate-names uses. Also doing ?loc=somegeneid in the url bar will also look in the plain generate-names index too, so if you want that then generate-names is still useful there. Technically all the stuff that generate-names does could be overridden directly (see Names API in jbrowse docs) but this plugin doesn't implement the Names API yet so doing both generate commands is useful

hsiaoyi0504 commented 6 years ago

Thanks