I have constantly used Galaxy to annotate some phage genomes. However, I have been trying to retrieve old data from Apollo into Galaxy for 3 weeks now with no success. I even uploaded the genome all over again, ran the structural workflow and re-called the genes on Apollo. However, again upon trying to retrieve the data to be able to run the functional workflow, the tool fails and attached is a screenshot of the error I received. I even tried to export the data directly from Apollo using the “Save track data” from the drop down menu of the user-created annotations but it also says “No such file or directory” (another screenshot attached). I don’t know what to do or who to contact, I emailed the galaxy support team but received no replies.
I would be extremely grateful if anyone can help! thanks a lot!
I am trying to share my history with you, but I probably need permission
I’m really glad you asked, and hopefully we can help!
How the Apollo application is hosted inside of Galaxy is a bit different from how other tools work! To get data out, try using this dedicated tool instead:
Please give this a try and let us know how it goes! Next time, please know you are welcome to ask questions for community help here whenever you get stuck!
Thanks a lot for your reply. This is exactly the tool I’ve tried “Retrieve data from Apollo into Galaxy” and the black screenshot in my message is the kind of error I get because it fails on all 6 outputs. I also tried the export thing directly from Apollo under the reference sequence tab but it’s not working as well; keeps running forever then nothing.
Ok, thanks for clarifying. In your other screenshots I noticed that all the visible annotations have a warning ! indicator. If you click on one of those, what is the message? Would you be able to screenshot it?
Also, if you would capture the job details under the i-info icon for 1) your original Apollo session from Create or Update Organism and 2) the run here with Retrieve Data, we can inspect to make sure that the tool is looking in the right place for your data. Screenshots can be enough.
And, this is unlikely to be the root issue (if this persisted for several weeks!), but just in case I’ll mention it: the UseGalaxy.eu server had some downtime yesterday, and everything may not be back up perfectly yet. So, I’ll run my check and if you could post back some screenshots, we can keep going this way.
One last thing, I tried something a short while ago and it seemed to work but still not entirely. In the Jbrowse viewer under the drop down menu of the “User-created annotations” I clicked on the edit configuration and there was this line that said “no export: true” so I changed that to false. It allowed me to save the data track as GFF3 file but without the genome. So I would still like to retrieve the features with the genome sequences if you know what I mean.
GTN 
