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apollo
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Tanya Berardini
Sep 19
Searching for own annotations
Hi all, As an admin, I can search for people annotations by name and status. For example: However, as
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Searching for own annotations
Hi all, As an admin, I can search for people annotations by name and status. For example: However, as
Sep 19
Tanya Berardini
,
Colin
3
Sep 6
Chromosome doesn't show up/load - simple solution?
Hi Colin, Thank you so much for your reply! We will try this and I'll report back on the results.
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Chromosome doesn't show up/load - simple solution?
Hi Colin, Thank you so much for your reply! We will try this and I'll report back on the results.
Sep 6
Michał T. Lorenc
,
Garrett Stevens
2
Sep 1
migrating users to new apollo
Hi Michał, The database format didn't change between 2.6.6 and 2.7.0, so you can load the
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migrating users to new apollo
Hi Michał, The database format didn't change between 2.6.6 and 2.7.0, so you can load the
Sep 1
Michael Thang
,
Nathan Dunn
2
Aug 24
can Jbrowse have both blat and blast search tool on the same machine?
It should work. NAthan On Aug 23, 2023, at 8:54 PM, Michael Thang <m.t...@qfab.org> wrote: Hi
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can Jbrowse have both blat and blast search tool on the same machine?
It should work. NAthan On Aug 23, 2023, at 8:54 PM, Michael Thang <m.t...@qfab.org> wrote: Hi
Aug 24
Michał T. Lorenc
, …
Tiffanie Nelson
3
Aug 9
registration page
Hi Michal, If you are from, or working with, an Australian-based research institute we have created
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registration page
Hi Michal, If you are from, or working with, an Australian-based research institute we have created
Aug 9
Taein Lee
,
Colin
2
May 16
PostgreSQL version question
Hi there, this was also mentioned here. https://github.com/GMOD/Apollo/issues/2660 If you can add
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PostgreSQL version question
Hi there, this was also mentioned here. https://github.com/GMOD/Apollo/issues/2660 If you can add
May 16
Antonin Thiébaut
, …
Colin
4
Apr 17
Importing itemRgb column of bed files
Hi Colin, Thanks for the advice, the BEDTabix track upload worked great! Antonin Le vendredi 14 avril
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Importing itemRgb column of bed files
Hi Colin, Thanks for the advice, the BEDTabix track upload worked great! Antonin Le vendredi 14 avril
Apr 17
Jeremy Volkening
Apr 14
questions on Apollo behavior/configuration
Hello, I've been testing Apollo for use in collaborative manual annotation of herpesvirus genomes
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questions on Apollo behavior/configuration
Hello, I've been testing Apollo for use in collaborative manual annotation of herpesvirus genomes
Apr 14
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