New Apollo Release 1.0.4(JB1.11.6)

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New Apollo Release 1.0.4(JB1.11.6)

Monica Munoz-Torres
Dear Colleagues, 

We would like to announce the Apollo release 1.0.4. 

If you currently have Web Apollo instances running, please be sure to read carefully through the updated documentation. Specially note: no more symlinking; please use property files instead.

We want to specially highlight an important update on how to access the new server for the Gene Ontology (annotating GO IDs in the "Information Editor"); please note that this URL update affects all previous versions of Apollo (details below). 

This latest release can be downloaded from GitHub:

The Readme contains steps for a Quick Update to version 1.0.x (note changes): 

Complete Apollo installation and configuration instructions for 1.0.x are available at: 

For a detailed account of all changes, please visit: 

These are a few highlighted changes:

+ Update to JBrowse 1.11.6 (
+ Added new Help page with Web Apollo specific content (#153).
+ Added Drupal authentication module to share authentication with an existing Drupal DB (#117).
+ Added a "Collapse" option to the "User-created Annotations" track. Track labels automatically removed. (#155).
+ Changed "maxHeight" on "User-created Annotations" track to prevent overflow (#124).

+ Updated ULR to new server to access Gene Ontology terms (GOLR). (#190). If you are not updating to 1.0.4, you can still patch it manually in AnnotTrack.js as shown here
+ Fixed an issue where the config files were readable by the outside world in previous 1.x versions.
+ Changed default user database to be encrypted. Unencrypted options are still available via command line scripts for people with older configurations (#147).
+ Fixed bug where Tomcat could report "Too many open files error" (#162).
+ Added MIME types for bigwig files (#166).
+ Fixed GFF3 export for non-specified phase, score, and strand (#177).
+ Fixed "Show track labels" causing feature labels go offscreen (#179).
+ Renamed "Edit Annotation" menu item to "Edit Information" and camel-case file-menu options. (#172)
+ Fixed "Add sequence search track" function not matching amino acid queries (#168).
+ Updated layout on changes page (#180).
+ Fixed problem with iFrame-embedded mode options (#183).
+ Fixed problem with "Add user" popup using outdated server configuration (#182).
+ Fixed minor issue raised when attempting to retrieve (non-existent) peptides from untranslated regions (#157).

If you are new to Apollo, we encourage you learn more about our software and its functionality by taking a tour of our Apollo Demo ( and exploring the User Guide (

We look forward to receiving your questions and suggestions. If you are not already part of the Apollo List, please join the conversation by providing your contact information on this form

The Apollo Development Team

Mentorship Matters!
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631

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