Some of our user’s (thanks Rob and Dan) have noted that we’ve changed the nature of our URL’s in Apollo 2.0.4. This is true!
https://<myserver>/Apollo/jbrowse/index.html?loc=scaffold_462:37133..37321&organism=<organism ID or Name>&tracks=gene_model
https://<myserver>/Apollo/<organism ID or Name>/jbrowse/index.html?loc=scaffold_462:37133..37321&tracks=gene_model
Note that you should be able to use the name or the organism ID.
Please let us know if you have any further problems or questions.
Nathan Dunn, PhD Berkeley Bioinformatics Open-source Projects (BBOP) Genomics Division, Lawrence Berkeley National Laboratory [hidden email]
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