apollo

I would raise an issue here: https://github.com/galaxy-genome-annotation/python-apollo I would let

Apollo 2.7.0 has been released: https://github.com/GMOD/Apollo/releases/tag/2.7.0 Features Add info

Begin forwarded message: From: Xiaomei Li <xiaome...@gmail.com> Subject: Re: [apollo]

So there are 2 issues: 1 - you have to pass in unique name as a JSON object within a JSON array (

Hi All, I'd like to understand what a successful annotation effort in Apollo looks like to better

How big? Might be that it is an excess of a web request and you'll need to configure it manually

I would rename the 2 keys so it overrides (ie, blat_nuc and blat_prot instead of blast_nuc and

Maybe set the type to Alignments2? (Canvas). Nathan > Begin forwarded message: > > From:

Hi all, It worked the whole time, but it took a long time. I solved the problem by compressing and

I think any of those should work, I'm just testing a local installation on my M1 iMac, thanks

Please feel free to retweet (hope I did it right): https://twitter.com/precogincog/status/

Disk space within the container might be another culprit as well as what the docker image itself

I would download and install JBrowse 1 and generate the names with that perl script and then point

Hi, sorry for the late reply. So, I'm using docker desktop, this morning I downloaded the new

Apollo 2.6.6 has been released: https://github.com/GMOD/Apollo/releases/tag/2.6.6 Features Update

If these red and green blocks are showing the actual soft clipped bases extending beyond where the

Are their server or client errors created when you click “read” for a particular user that is not the

Thanks you, I was Indeed looking to search from within the jbrowse directory for non-annotated genes.

Ok, good to know. That means that Chrome probably has something in its cache that is causing the

Hi Stevens, I did a test, I download the gff3 of D. melanogaster, compressed it as you suggested and

Hi, I'm very new to apollo/jbrowse, and I'm trying to understand how to create my tracks, and

Hi Stevens, I think I managed, I had "transcript" instead of "mRNA" in my gff3,

Thanks Colin, reloading the file with --type mRNA did indeed filter out the box from being displayed.

Thanks for the update. If you're able to let us know if it works, we can try to get our docker

PS I added it also to [GitHub issues](https://github.com/GMOD/Apollo/issues/2643) On Wed, Mar 9, 2022

Hi there, I think you probably have the right idea! Saw your email to my personal account. The

Oh, sorry for not reading that properly. You are right. Nathan On Feb 22, 2022, at 12:34 PM, Colin

NHi Nathan, No trade secrets :) it is a very fancy alias! Where do I find errors? On Fri, Feb 18,

Thank you for your reply. I don't currently have access to Docker. I'll try to get one.

There's some discussion https://github.com/GMOD/Apollo/issues/2640 here if it helps! Ciao, Helena