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Nathan Dunn
Mar 7
Re: [apollo] New install error
I would raise an issue here: https://github.com/galaxy-genome-annotation/python-apollo I would let
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Re: [apollo] New install error
I would raise an issue here: https://github.com/galaxy-genome-annotation/python-apollo I would let
Mar 7
Garrett Stevens
Jan 3
Apollo 2.7.0 released
Apollo 2.7.0 has been released: https://github.com/GMOD/Apollo/releases/tag/2.7.0 Features Add info
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Apollo 2.7.0 released
Apollo 2.7.0 has been released: https://github.com/GMOD/Apollo/releases/tag/2.7.0 Features Add info
Jan 3
Nathan Dunn
12/6/22
Fwd: [apollo] Download all the manual correction/curation history records from Apollo
Begin forwarded message: From: Xiaomei Li <xiaome...@gmail.com> Subject: Re: [apollo]
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Fwd: [apollo] Download all the manual correction/curation history records from Apollo
Begin forwarded message: From: Xiaomei Li <xiaome...@gmail.com> Subject: Re: [apollo]
12/6/22
Xiaomei Li
,
Nathan Dunn
4
11/14/22
Download all the manual correction/curation history records from Apollo
So there are 2 issues: 1 - you have to pass in unique name as a JSON object within a JSON array (
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Download all the manual correction/curation history records from Apollo
So there are 2 issues: 1 - you have to pass in unique name as a JSON object within a JSON array (
11/14/22
Rad
10/27/22
Looking for lively (or at least once lively) annotation efforts / apollo instances
Hi All, I'd like to understand what a successful annotation effort in Apollo looks like to better
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Looking for lively (or at least once lively) annotation efforts / apollo instances
Hi All, I'd like to understand what a successful annotation effort in Apollo looks like to better
10/27/22
Michał T. Lorenc
,
Nathan Dunn
2
9/18/22
Logged out or server failure. Attempt to reconnect?
How big? Might be that it is an excess of a web request and you'll need to configure it manually
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Logged out or server failure. Attempt to reconnect?
How big? Might be that it is an excess of a web request and you'll need to configure it manually
9/18/22
Michał T. Lorenc
,
Nathan Dunn
7
8/31/22
BLAT removing
I would rename the 2 keys so it overrides (ie, blat_nuc and blat_prot instead of blast_nuc and
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BLAT removing
I would rename the 2 keys so it overrides (ie, blat_nuc and blat_prot instead of blast_nuc and
8/31/22
Michał T. Lorenc
,
Nathan Dunn
2
8/19/22
BAM file track
Maybe set the type to Alignments2? (Canvas). Nathan > Begin forwarded message: > > From:
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BAM file track
Maybe set the type to Alignments2? (Canvas). Nathan > Begin forwarded message: > > From:
8/19/22
Michał T. Lorenc
,
Nathan Dunn
4
7/25/22
File not found trackData.jsonz
Hi all, It worked the whole time, but it took a long time. I solved the problem by compressing and
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File not found trackData.jsonz
Hi all, It worked the whole time, but it took a long time. I solved the problem by compressing and
7/25/22
Christopher Fields
,
Nathan Dunn
3
7/20/22
Test data issues
I think any of those should work, I'm just testing a local installation on my M1 iMac, thanks
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Test data issues
I think any of those should work, I'm just testing a local installation on my M1 iMac, thanks
7/20/22
Robert Buels
,
Nathan Dunn
2
7/14/22
Position open working on Apollo at Glasgow
Please feel free to retweet (hope I did it right): https://twitter.com/precogincog/status/
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Position open working on Apollo at Glasgow
Please feel free to retweet (hope I did it right): https://twitter.com/precogincog/status/
7/14/22
Marc Hoeppner
, …
Nathan Dunn
3
7/7/22
Docker - web service becomes unresponsive after some time
Disk space within the container might be another culprit as well as what the docker image itself
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Docker - web service becomes unresponsive after some time
Disk space within the container might be another culprit as well as what the docker image itself
7/7/22
Johannes Debler
,
Nathan Dunn
3
6/2/22
Find annotation in tracks
I would download and install JBrowse 1 and generate the names with that perl script and then point
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Find annotation in tracks
I would download and install JBrowse 1 and generate the names with that perl script and then point
6/2/22
Francesco Cicconardi
,
Nathan Dunn
3
5/11/22
Apollo with Docker with M1 chip
Hi, sorry for the late reply. So, I'm using docker desktop, this morning I downloaded the new
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Apollo with Docker with M1 chip
Hi, sorry for the late reply. So, I'm using docker desktop, this morning I downloaded the new
5/11/22
Garrett Stevens
5/10/22
Apollo 2.6.6 released
Apollo 2.6.6 has been released: https://github.com/GMOD/Apollo/releases/tag/2.6.6 Features Update
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Apollo 2.6.6 released
Apollo 2.6.6 has been released: https://github.com/GMOD/Apollo/releases/tag/2.6.6 Features Update
5/10/22
Johannes Debler
,
Colin
3
4/25/22
highlight polyA/polyT clipped reads
If these red and green blocks are showing the actual soft clipped bases extending beyond where the
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highlight polyA/polyT clipped reads
If these red and green blocks are showing the actual soft clipped bases extending beyond where the
4/25/22
uguyet
,
Nathan Dunn
2
4/19/22
Permissions issue
Are their server or client errors created when you click “read” for a particular user that is not the
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Permissions issue
Are their server or client errors created when you click “read” for a particular user that is not the
4/19/22
uguyet
,
Nathan Dunn
3
4/8/22
search by gene name
Thanks you, I was Indeed looking to search from within the jbrowse directory for non-annotated genes.
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search by gene name
Thanks you, I was Indeed looking to search from within the jbrowse directory for non-annotated genes.
4/8/22
Monica Poelchau
, …
Garrett Stevens
16
4/8/22
some users can't update the gene name field
Ok, good to know. That means that Chrome probably has something in its cache that is causing the
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some users can't update the gene name field
Ok, good to know. That means that Chrome probably has something in its cache that is causing the
4/8/22
Francesco Cicconardi
,
Garrett Stevens
6
3/25/22
Apollo is very slow with GFF3 track
Hi Stevens, I did a test, I download the gff3 of D. melanogaster, compressed it as you suggested and
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Apollo is very slow with GFF3 track
Hi Stevens, I did a test, I download the gff3 of D. melanogaster, compressed it as you suggested and
3/25/22
Francesco Cicconardi
3/24/22
Portcullis splice sites
Hi, I'm very new to apollo/jbrowse, and I'm trying to understand how to create my tracks, and
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Portcullis splice sites
Hi, I'm very new to apollo/jbrowse, and I'm trying to understand how to create my tracks, and
3/24/22
Michał T. Lorenc
, …
Francesco Cicconardi
7
3/24/22
an error was encountered when displaying this track
Hi Stevens, I think I managed, I had "transcript" instead of "mRNA" in my gff3,
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an error was encountered when displaying this track
Hi Stevens, I think I managed, I had "transcript" instead of "mRNA" in my gff3,
3/24/22
Johannes Debler
, …
Colin
6
3/22/22
remove 'transcript' track
Thanks Colin, reloading the file with --type mRNA did indeed filter out the box from being displayed.
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remove 'transcript' track
Thanks Colin, reloading the file with --type mRNA did indeed filter out the box from being displayed.
3/22/22
Christopher Tabone
,
Garrett Stevens
3
3/16/22
Upgrading Tomcat in Docker image?
Thanks for the update. If you're able to let us know if it works, we can try to get our docker
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Upgrading Tomcat in Docker image?
Thanks for the update. If you're able to let us know if it works, we can try to get our docker
3/16/22
Michał T. Lorenc
2
3/9/22
Get gene sequence
PS I added it also to [GitHub issues](https://github.com/GMOD/Apollo/issues/2643) On Wed, Mar 9, 2022
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Get gene sequence
PS I added it also to [GitHub issues](https://github.com/GMOD/Apollo/issues/2643) On Wed, Mar 9, 2022
3/9/22
Abhijit Sanyal
,
Colin
2
3/8/22
Searches in Apollo using centimorgan distances
Hi there, I think you probably have the right idea! Saw your email to my personal account. The
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Searches in Apollo using centimorgan distances
Hi there, I think you probably have the right idea! Saw your email to my personal account. The
3/8/22
Johannes Debler
, …
Nathan Dunn
4
2/22/22
change genetic code (for mitochondria)
Oh, sorry for not reading that properly. You are right. Nathan On Feb 22, 2022, at 12:34 PM, Colin
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change genetic code (for mitochondria)
Oh, sorry for not reading that properly. You are right. Nathan On Feb 22, 2022, at 12:34 PM, Colin
2/22/22
Sofia Robb
,
Nathan Dunn
3
2/18/22
issues with adding an alias
NHi Nathan, No trade secrets :) it is a very fancy alias! Where do I find errors? On Fri, Feb 18,
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issues with adding an alias
NHi Nathan, No trade secrets :) it is a very fancy alias! Where do I find errors? On Fri, Feb 18,
2/18/22
Cen T
,
Garrett Stevens
3
1/6/22
running docker image in singularity
Thank you for your reply. I don't currently have access to Docker. I'll try to get one.
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running docker image in singularity
Thank you for your reply. I don't currently have access to Docker. I'll try to get one.
1/6/22
Alina Mikhailova
,
Helena Rasche
2
12/17/21
log4j vulnerability
There's some discussion https://github.com/GMOD/Apollo/issues/2640 here if it helps! Ciao, Helena
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log4j vulnerability
There's some discussion https://github.com/GMOD/Apollo/issues/2640 here if it helps! Ciao, Helena
12/17/21