Migrating from GBrowse to JBrowse

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Things to consider

New or Existing Server

disk space requirements

computing requirements

The computing requirements for a JBrowse server are generally much less than a GBrowse server, since the JBrowse server will only be serving up small bits of text as json and javascript files, as opposed to creating images on the fly for GBrowse servers. On the other hand, processing the data to create the JBrowse server is generally more intensive (or at a minimum, as much as) that what is needed for a GBrowse instance. It is not unreasonable therefore to have a server with a fair amount of resources for doing the data processing and then using a "smaller" server for serving the data. In fact, it is possible to put all of the data in an AWS S3 store and not have a server at all once the data processing is done. See Using_AWS_S3_For_JBrowse.

do you have the original GFF?

Generally, it Is easier to create a JBrowse instance from the original GFF that from a GBrowse database like Bio::DB::GFF or Bio::DB::SeqFeature::Store.

dealing with multiple species/data sources

JBrowse can easily support having multiple species or data sources, like you would see in a drop down menu in GBrowse. See this FAQ and the one below it, and the section in the JBrowse Configuration Guide that they point to.


Example command lines for GFF, FASTA and BioDB


Mapping out GBrowse to JBrowse configuration

A table would be good

Special note about callbacks

Dealing with binary data

Where to get help