Howdy all!
As most of you know, we pushed out some major upgrades to our main services, Galaxy and Apollo, this past Monday. It gave us many new features such as propagating dataset nametags, upgraded workflow management, faster UI for both services, additional annotation control in Apollo, and many more (that will be in a future post) but this will be covering the things that aren’t quite working yet.
Our admin team is currently aware and working on these issues, if you come across something else please report them to the team through the main Galaxy bug report system, or via email or github otherwise. If you have a failed job that matches one of these issues, please try re-running the job before contacting the admin team.
2020-08-24 Noon CST: Apollo is currently down to apply further updates to try and resolve some of the below issues, we will update here on progress and estimates.
Apollo access has been restored, but may have momentary disconnection for restarting with new settings as we continue working on solutions.
KNOWN ISSUES:
- Galaxy
- Failure when Saving Workflow with
Uncaught exception in exposed API method
- Failure when Saving Workflow with
- Apollo
- Annotation list and editor does not load: Try logging out, closing browser window, clearing cache, etc. If none of this solves it, please contact admin team
- InterproScan evidence does not display properly with some entries displaying invisible until moused over
- TMHMM evidence does not display Transmembrane Domain subfeatures correctly
- [RESOLVED] Protein BLAST Tracks fail to load: Currently investigating solutions for this issue.
- Structural and Functional Workflow
We are working to update the shared workflows to the new tooling.- [RESOLVED] Create Or Update Organism in Apollo failure with
504 Gateway Timeout
- [RESOLVED] Create Or Update Organism in Apollo failure with
java.lang.NullPointerException: Cannot get property 'organism' on null object
- [RESOLVED] Create Or Update Organism in Apollo failure with
PermissionError: [Errno 13] Permission denied: '/opt/apollo'
- [RESOLVED] tRNAScan, Aragorn, Glimmer3 failure with
SyntaxError: Missing parenthesis in call to 'print'
- [RESOLVED] Fix tRNA Model failure with
KeyError: 'Codon'
- [RESOLVED] Create Or Update Organism in Apollo failure with
PermissionError: [Errno 13] Permission denied: '/opt/apollo'
- [RESOLVED] Create Or Update Organism in Apollo failure with
- General Tools
- [RESOLVED] Share Organism With User webapollo tool unavailable
- [RESOLVED] Retrieve Data from Apollo no longer provides full genomic sequence fasta file (The GFF3 file includes an appended fasta file. We now have a tool to split this into two datasets if needed)
- [RESOLVED] All tools failure with
condor_submit failed
- [RESOLVED] Filter sequences by length failure with
SyntaxError: Missing parenthesis in call to 'print'
- [RESOLVED] ClustalW failure with
Invalid Syntax
- [RESOLVED] Retrieve JBrowse failure with
Missing seq directory BEFORE copy