gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Thank you so much for your feedback Colin! It all makes sense now.

Vaneet

From: Colin <col...@gm...>
Sent: December 1, 2025 10:33 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

>Thank you for adding that feature so quickly, I really appreciate it! From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

Yes, if you make invisible html, it will not show up, but can affect sorting. Note that visible HTML will show up. The HTML decoding was already available for track names but the link i sent added it for track categories also

>.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

That is a fine way to do it. I encourage making custom scripts to edit the config.json, it is challenging to encode every possible situation into the @jbrowse/cli tool. You also  don't even really have to use add-track-json if you want, you can just write a script to directly edit the config.json

>When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Example of this here https://github.com/GMOD/jbrowse-components/discussions/3879#discussioncomment-6855563

-Colin


On Mon, Dec 1, 2025 at 1:44 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Thank you for adding that feature so quickly, I really appreciate it!

From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

While we’re discussing JBrowse features, I need some help with Multi-Quantitative tracks; we can always discuss in an online meeting if that works better.  I needed a way to add some MultiBigWig tracks via command-line as I’m using a script so I didn’t want to do it the manual way of entering a new track stanza into the main config.json file.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

Anyways, when configuring the track, I followed what was covered in the documentation which uses the MultiWiggleAdapter:

https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/

When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Thanks,

Vaneet
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: November 29, 2025 5:55 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264 that may help with this. It should be out in the next release, which i'm hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically ‘<span>’ with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I’ve tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I’m attempting to order categories by development stage not stage # so alphabetical won’t work.  Please let me know if there’s a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Colin <col...@gm...>]

>Thank you for adding that feature so quickly, I really appreciate it! From
the name of the add-on, I’m going to assume it does what I was talking
about from the previous JBrowse?  It allows HTML to be added to track names
and then in turn decodes the HTML so it doesn’t visibly show up, is that
correct? Or is it a different behaviour?

Yes, if you make invisible html, it will not show up, but can affect
sorting. Note that visible HTML will show up. The HTML decoding was already
available for track names but the link i sent added it for track categories
also

>.  I thought the best way was to create a new .json file via the script
that contains the new MultiBigWig track and use the add-track-json command
to add that ‘track JSON’ file to the main config.json with all the other
tracks.  Is that the best way or is there a better way to do it via the
command-line or a different command?

That is a fine way to do it. I encourage making custom scripts to edit
the config.json, it is challenging to encode every possible situation into
the @jbrowse/cli tool. You also  don't even really have to use
add-track-json if you want, you can just write a script to directly edit
the config.json

>When added this seems to draw the track using the ‘multirowxy’ renderer
type.  My primary question here is how can I change the configuration to
draw the track using one of the other renderer types (xyplot,
multirowdensity, multiline, multirowline)?  I’m specifically looking to
draw it as an xyplot but I’d be interested in how to configure all of the
types.  Do I need to change the adapter type?



Example of this here
https://github.com/GMOD/jbrowse-components/discussions/3879#discussioncomment-6855563


-Colin


On Mon, Dec 1, 2025 at 1:44 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Thank you for adding that feature so quickly, I really appreciate it!
>
>
>
> From the name of the add-on, I’m going to assume it does what I was
> talking about from the previous JBrowse?  It allows HTML to be added to
> track names and then in turn decodes the HTML so it doesn’t visibly show
> up, is that correct? Or is it a different behaviour?
>
>
>
> While we’re discussing JBrowse features, I need some help with
> Multi-Quantitative tracks; we can always discuss in an online meeting if
> that works better.  I needed a way to add some MultiBigWig tracks via
> command-line as I’m using a script so I didn’t want to do it the manual way
> of entering a new track stanza into the main config.json file.  I thought
> the best way was to create a new .json file via the script that contains
> the new MultiBigWig track and use the add-track-json command to add that
> ‘track JSON’ file to the main config.json with all the other tracks.  Is
> that the best way or is there a better way to do it via the command-line or
> a different command?
>
>
>
> Anyways, when configuring the track, I followed what was covered in the
> documentation which uses the MultiWiggleAdapter:
>
>
>
> https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/
>
>
>
> When added this seems to draw the track using the ‘multirowxy’ renderer
> type.  My primary question here is how can I change the configuration to
> draw the track using one of the other renderer types (xyplot,
> multirowdensity, multiline, multirowline)?  I’m specifically looking to
> draw it as an xyplot but I’d be interested in how to configure all of the
> types.  Do I need to change the adapter type?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> *From:* Colin <col...@gm...>
> *Sent:* November 29, 2025 5:55 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: JBrowse2 sorting track categories with HTML or otherwise?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
> I made a change here https://github.com/GMOD/jbrowse-components/pull/5264
> that may help with this. It should be out in the next release, which i'm
> hoping won't be too long
>
>
>
> You can try it with
>
>
>
> jbrowse create --nightly newinstance
>
>
>
>
>
> -Colin
>
>
>
> On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
>
>
> In the original JBrowse, when I had a large assortment of tracks and I
> wanted to sort them in an order other then alphabetical or the position in
> the config file from where they were added, I used HTML tags in the track
> names.  Basically ‘<span>’ with the name attribute being given a number to
> assign the order of the track in the category it belongs to.  I did the
> same for track categories.
>
>
>
> In JBrowse2 I’ve tried the same technique for track names, and it works by
> decoding the HTML tags and not actually showing the raw HTML in the visible
> track names.  This method does not work for categories when I try it as the
> HTML is not decoded and just shown as is in the category name.  So,  does
> anyone know a better way to sort categories besides alphabetical order?
> This becomes relevant where for Xenopus I’m attempting to order categories
> by development stage not stage # so alphabetical won’t work.  Please let me
> know if there’s a better way to do this in JBrowse2.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>
>
>

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Hey Colin,

Thank you for adding that feature so quickly, I really appreciate it!

From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

While we’re discussing JBrowse features, I need some help with Multi-Quantitative tracks; we can always discuss in an online meeting if that works better.  I needed a way to add some MultiBigWig tracks via command-line as I’m using a script so I didn’t want to do it the manual way of entering a new track stanza into the main config.json file.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

Anyways, when configuring the track, I followed what was covered in the documentation which uses the MultiWiggleAdapter:

https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/

When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Thanks,

Vaneet
From: Colin <col...@gm...>
Sent: November 29, 2025 5:55 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264 that may help with this. It should be out in the next release, which i'm hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically ‘<span>’ with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I’ve tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I’m attempting to order categories by development stage not stage # so alphabetical won’t work.  Please let me know if there’s a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Colin <col...@gm...>]

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264
that may help with this. It should be out in the next release, which i'm
hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi all,
>
>
>
> In the original JBrowse, when I had a large assortment of tracks and I
> wanted to sort them in an order other then alphabetical or the position in
> the config file from where they were added, I used HTML tags in the track
> names.  Basically ‘<span>’ with the name attribute being given a number to
> assign the order of the track in the category it belongs to.  I did the
> same for track categories.
>
>
>
> In JBrowse2 I’ve tried the same technique for track names, and it works by
> decoding the HTML tags and not actually showing the raw HTML in the visible
> track names.  This method does not work for categories when I try it as the
> HTML is not decoded and just shown as is in the category name.  So,  does
> anyone know a better way to sort categories besides alphabetical order?
> This becomes relevant where for Xenopus I’m attempting to order categories
> by development stage not stage # so alphabetical won’t work.  Please let me
> know if there’s a better way to do this in JBrowse2.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>
>

[Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically '<span>' with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I've tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I'm attempting to order categories by development stage not stage # so alphabetical won't work.  Please let me know if there's a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] How to add more fields to faceted selector

[Colin <col...@gm...>]

The basic idea for the faceted track selector is that any "top level" entry
in the track metadata becomes searchable in the track metadata.  Example

{
      "type": "VariantTrack",
      "trackId": "volvox_test_vcf",
      "metadata": {
        "thing here": "hello"
      },
      "name": "volvox 1000genomes vcf",
      "assemblyNames": ["volvox"],
      "category": ["Variants"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "volvox.test.vcf.gz"
      }
    },

That will make "thing here" a column and a facet filter, but also note that
it filters out "sparse" metadata columns by default, so it only shows
metadata that is shared across >5 tracks as a facet (arbitrary threshold)

You can toggle "Show sparse metadata columns" to show facets for even
metadata not shared by 5 tracks

[image: image.png]



There is no notion of only a subset of tracks appearing in the faceted
selector currently

-Colin

On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi,
>
>
>
> There is documentation for adding the field ‘category’ as an active field
> to the faceted track selector.  How do you add more fields to that so they
> can be used to filter tracks for in that pop up window?  I tried added some
> random fields under the ‘metadata{}’ name in the config.json file.  While
> they appear in the ‘About this track’ dialog they don’t appear in the
> faceted track selector.
>
>
>
> Also, is there a way I can limit which tracks I want to appear in the
> faceted track selector?  I want a subset of tracks that can appear in their
> own faceted track selector with many metadata fields to filter upon similar
> to the original JBrowse.  How do I do this in JBrowse 2?
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] How to add more fields to faceted selector

[Vaneet L. <van...@uc...>]

Hi,

There is documentation for adding the field 'category' as an active field to the faceted track selector.  How do you add more fields to that so they can be used to filter tracks for in that pop up window?  I tried added some random fields under the 'metadata{}' name in the config.json file.  While they appear in the 'About this track' dialog they don't appear in the faceted track selector.

Also, is there a way I can limit which tracks I want to appear in the faceted track selector?  I want a subset of tracks that can appear in their own faceted track selector with many metadata fields to filter upon similar to the original JBrowse.  How do I do this in JBrowse 2?

Thanks,

Vaneet

Re: [Gmod-ajax] Gene search result remains

[Colin <col...@gm...>]

(note that you can also change the entire "session title" in the same way
by clicking where it says "New session ..." on the top level blue
navigation bar)


-Colin

On Fri, Jun 27, 2025 at 3:07 PM Colin <col...@gm...> wrote:

> I don't believe this is currently possible. However, if this is just for
> screenshot purposes or just to remember what was searched, note that you
> can manually edit the "View title" in the purple bar view header.
>
> For example, see the screenshot below: It says "My custom text here" in
> the view header, just due to me clicking the view header text and typing to
> make my own custom title
>
> [image: image.png]
>
> Hope that helps
>
> -Colin
>
> On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hi,
>>
>>
>>
>> My PI was curious about something in JBrowse2.  When you enter a search
>> result in the location box and visit the location where the gene is in the
>> genome, is it possible to allow the search results to remain in the search
>> box instead of it switching automatically to the genome coordinates?  Or
>> perhaps can the gene search result remain anywhere in that top panel after
>> you've visited your gene of interest.  I assume this isn't possible but
>> just thought I'd ask if there's a plugin for it perhaps.
>>
>> Thanks,
>>
>> Vaneet
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Gene search result remains

[Colin <col...@gm...>]

I don't believe this is currently possible. However, if this is just for
screenshot purposes or just to remember what was searched, note that you
can manually edit the "View title" in the purple bar view header.

For example, see the screenshot below: It says "My custom text here" in the
view header, just due to me clicking the view header text and typing to
make my own custom title

[image: image.png]

Hope that helps

-Colin

On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...>
wrote:

> Hi,
>
>
>
> My PI was curious about something in JBrowse2.  When you enter a search
> result in the location box and visit the location where the gene is in the
> genome, is it possible to allow the search results to remain in the search
> box instead of it switching automatically to the genome coordinates?  Or
> perhaps can the gene search result remain anywhere in that top panel after
> you've visited your gene of interest.  I assume this isn't possible but
> just thought I'd ask if there's a plugin for it perhaps.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Gene search result remains

[Vaneet L. <van...@uc...>]

Hi,



My PI was curious about something in JBrowse2.  When you enter a search result in the location box and visit the location where the gene is in the genome, is it possible to allow the search results to remain in the search box instead of it switching automatically to the genome coordinates?  Or perhaps can the gene search result remain anywhere in that top panel after you've visited your gene of interest.  I assume this isn't possible but just thought I'd ask if there's a plugin for it perhaps.

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 VCF track

[Colin <col...@gm...>]

Currently there is no option for this. Potential could add it though!

If you can make a github issue for it that would be great
-Colin

On Thu, May 29, 2025 at 2:54 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I'd like to know whether it is possible to turn off the rendering of the
> "genotype" column for a VCF track in the feature details in the track
> configuration. Looks like as a user viewing the track, we can click the
> "columns" button to select the columns to show. But is there a way to
> selectively hide columns in the backend of track configuration, so by
> default users would only see certain columns of VCF INFO fields?
>
> For an example, see attached screenshot. We'd like to show only "sample"
> and "GT" by default, no "genotype" column.
>
> Thanks!
>
> Ke
> [image: Screenshot 2025-05-29 at 1.48.16 PM.png]
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 VCF track

[Ke J. <bio...@gm...>]

Hi,

I'd like to know whether it is possible to turn off the rendering of the
"genotype" column for a VCF track in the feature details in the track
configuration. Looks like as a user viewing the track, we can click the
"columns" button to select the columns to show. But is there a way to
selectively hide columns in the backend of track configuration, so by
default users would only see certain columns of VCF INFO fields?

For an example, see attached screenshot. We'd like to show only "sample"
and "GT" by default, no "genotype" column.

Thanks!

Ke
[image: Screenshot 2025-05-29 at 1.48.16 PM.png]

Re: [Gmod-ajax] JBrowse subfeatures repeating bug?

[Vaneet L. <van...@uc...>]

Hey Colin,

Here’s an example for the hhat gene:

https://jbrowse.xenbase.org/XenJBrowse/?data=data%2Fxt10_0&loc=Chr5%3A15519428..15720936&tracks=DNA%2CXT10_0_Xenbase%2CgRNAs&highlight=

If you click on the gene models and then ‘show subfeatures’, you can see the UTR being repeated several times, which isn’t present in the GFF3 file itself.  Most models with UTRs show this repeated issue.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: May 12, 2025 1:35 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: JBrowse subfeatures repeating bug?

[△EXTERNAL]

If you can send a link it may help

-Colin

On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi Colin,

Have you ever encountered this bug below in JBrowse when using ‘NCBI’ style GFF3s with implied UTRs to be drawn in the JBrowse tracks?

Anyone else ever run into this issue?  I’m just wondering if there’s something that can be done to prevent it from repeating like that.  I can give a direct link to someone if they want to see the issue live and recreate it.

Thanks,

Vaneet

From: Vaneet Lotay
Sent: April 9, 2025 10:51 AM
To: gmo...@li...<mailto:gmo...@li...>
Subject: JBrowse subfeatures repeating bug?

Hi,

I’m not sure if anyone’s already run into this bug before, at least it certainly seems like a bug.  When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached).  It doesn’t matter which model I select or even under which species or genome for that matter that it’s under, it always appears repeated like that in the details window.  Here’s a trimmed down version of the hhex.S gene that’s in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:

Chr7S   Gnomon  gene    15890549        15902647        .       -       .       ID=XBXL10_1g32594;Name=hhex.S
Chr7S   Gnomon  mRNA    15890549        15902647        .       -       .       ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S   Gnomon  exon    15902179        15902647        .       -       .       ID=XBexon785823;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15896206        15896384        .       -       .       ID=XBexon785824;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15894761        15894811        .       -       .       ID=XBexon785825;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15890549        15891175        .       -       .       ID=XBexon785826;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15902179        15902551        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15896206        15896384        .       -       2       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15894761        15894811        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15890948        15891175        .       -       0       ID=XBcds718348;Parent=XBmRNA61523

I have this setting enabled in my track to draw out the ‘implied’ UTRs which aren’t directly supplied in the GFF3 file:

        "impliedUTRs" : true,

Has anyone run into this before?  Is it a technical bug?  Why is it happening?

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse subfeatures repeating bug?

[Colin <col...@gm...>]

If you can send a link it may help

-Colin

On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi Colin,
>
>
>
> Have you ever encountered this bug below in JBrowse when using ‘NCBI’
> style GFF3s with implied UTRs to be drawn in the JBrowse tracks?
>
>
>
> Anyone else ever run into this issue?  I’m just wondering if there’s
> something that can be done to prevent it from repeating like that.  I can
> give a direct link to someone if they want to see the issue live and
> recreate it.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay
> *Sent:* April 9, 2025 10:51 AM
> *To:* gmo...@li...
> *Subject:* JBrowse subfeatures repeating bug?
>
>
>
> Hi,
>
>
>
> I’m not sure if anyone’s already run into this bug before, at least it
> certainly seems like a bug.  When I click on my gene model in JBrowse, and
> then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR
> segment gets displayed multiple times as duplicates with the same
> coordinates (screenshot attached).  It doesn’t matter which model I select
> or even under which species or genome for that matter that it’s under, it
> always appears repeated like that in the details window.  Here’s a trimmed
> down version of the hhex.S gene that’s in the screenshot from my GFF3
> (column 9 attributes trimmed off) just so it can fit here:
>
>
>
> Chr7S   Gnomon  gene    15890549        15902647        .       -
> .       ID=XBXL10_1g32594;Name=hhex.S
>
> Chr7S   Gnomon  mRNA    15890549        15902647        .       -
> .       ID=XBmRNA61523;Parent=XBXL10_1g32594
>
> Chr7S   Gnomon  exon    15902179        15902647        .       -
> .       ID=XBexon785823;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15896206        15896384        .       -
> .       ID=XBexon785824;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15894761        15894811        .       -
> .       ID=XBexon785825;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15890549        15891175        .       -
> .       ID=XBexon785826;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15902179        15902551        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15896206        15896384        .       -
> 2       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15894761        15894811        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15890948        15891175        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
>
>
> I have this setting enabled in my track to draw out the ‘implied’ UTRs
> which aren’t directly supplied in the GFF3 file:
>
>
>
>         "impliedUTRs" : true,
>
>
>
> Has anyone run into this before?  Is it a technical bug?  Why is it
> happening?
>
>
>
> Thanks,
>
>
> Vaneet
>

Re: [Gmod-ajax] JBrowse subfeatures repeating bug?

[Vaneet L. <van...@uc...>]

Hi Colin,

Have you ever encountered this bug below in JBrowse when using 'NCBI' style GFF3s with implied UTRs to be drawn in the JBrowse tracks?

Anyone else ever run into this issue?  I'm just wondering if there's something that can be done to prevent it from repeating like that.  I can give a direct link to someone if they want to see the issue live and recreate it.

Thanks,

Vaneet

From: Vaneet Lotay
Sent: April 9, 2025 10:51 AM
To: gmo...@li...
Subject: JBrowse subfeatures repeating bug?

Hi,

I'm not sure if anyone's already run into this bug before, at least it certainly seems like a bug.  When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3'UTR or 5'UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached).  It doesn't matter which model I select or even under which species or genome for that matter that it's under, it always appears repeated like that in the details window.  Here's a trimmed down version of the hhex.S gene that's in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:

Chr7S   Gnomon  gene    15890549        15902647        .       -       .       ID=XBXL10_1g32594;Name=hhex.S
Chr7S   Gnomon  mRNA    15890549        15902647        .       -       .       ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S   Gnomon  exon    15902179        15902647        .       -       .       ID=XBexon785823;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15896206        15896384        .       -       .       ID=XBexon785824;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15894761        15894811        .       -       .       ID=XBexon785825;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15890549        15891175        .       -       .       ID=XBexon785826;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15902179        15902551        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15896206        15896384        .       -       2       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15894761        15894811        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15890948        15891175        .       -       0       ID=XBcds718348;Parent=XBmRNA61523

I have this setting enabled in my track to draw out the 'implied' UTRs which aren't directly supplied in the GFF3 file:

        "impliedUTRs" : true,

Has anyone run into this before?  Is it a technical bug?  Why is it happening?

Thanks,

Vaneet

[Gmod-ajax] Apollo 2.8.1 released

[Garrett S. <ste...@gm...>]

Apollo 2.8.1 has been released: 
https://github.com/GMOD/Apollo/releases/tag/2.8.1

*Bug Fixes*

   - Fix not being able to see or add users in the UI when no organisms 
   have been added yet. 2666 <https://github.com/GMOD/Apollo/pull/2666>.
   - Fix blat search not working in Docker image. 2670 
   <https://github.com/GMOD/Apollo/pull/2670>.

Full change long for all versions can be found here: 
https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details: 
http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here: 
https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found.
Active mailing list (ap...@lb...) and google group 
<https://groups.google.com/a/lbl.gov/g/apollo>.

Re: [Gmod-ajax] JBrowse2 config file

[Ke J. <bio...@gm...>]

We’ve had the same problem of one single config.json getting too many
tracks and becoming too big to manage. We ended up establishing multiple
instances of JBrowse2 for different user groups. I think that is an option
to have multiple more manageable config.json files.

Ke

On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I was curious when working with JBrowse2, is it very easy or user-friendly
> to setup multiple config.json files for the different genomes that may be
> hosted in the browser, similar to the original JBrowse?  If so, then please
> explain what the best way to do that is.  Or is JBrowse2 basically built to
> work best with one central config.json file as it is by default?
>
>
>
> Thanks,
>
> <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>
>
>
>
> <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW
> <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>*
>
> *Calgary, AB T2N 1N4
> <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>*
>
> *CANADA
> <https://www.google.com/maps/search/2500+University+Drive+NW+%0D%0A+Calgary,+AB+T2N+1N4+%0D%0A+CANADA?entry=gmail&source=g>*
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse subfeatures repeating bug?

[Vaneet L. <van...@uc...>]

Hi,

I'm not sure if anyone's already run into this bug before, at least it certainly seems like a bug.  When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3'UTR or 5'UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached).  It doesn't matter which model I select or even under which species or genome for that matter that it's under, it always appears repeated like that in the details window.  Here's a trimmed down version of the hhex.S gene that's in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:

Chr7S   Gnomon  gene    15890549        15902647        .       -       .       ID=XBXL10_1g32594;Name=hhex.S
Chr7S   Gnomon  mRNA    15890549        15902647        .       -       .       ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S   Gnomon  exon    15902179        15902647        .       -       .       ID=XBexon785823;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15896206        15896384        .       -       .       ID=XBexon785824;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15894761        15894811        .       -       .       ID=XBexon785825;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15890549        15891175        .       -       .       ID=XBexon785826;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15902179        15902551        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15896206        15896384        .       -       2       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15894761        15894811        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15890948        15891175        .       -       0       ID=XBcds718348;Parent=XBmRNA61523

I have this setting enabled in my track to draw out the 'implied' UTRs which aren't directly supplied in the GFF3 file:

        "impliedUTRs" : true,

Has anyone run into this before?  Is it a technical bug?  Why is it happening?

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 config file

[Vaneet L. <van...@uc...>]

Thanks for that great info!

I find it cleaner having different config files but if it loses the ability to compare multiple genomes at once, I don’t think it’s worth it.  I’ll probably stick to one main config.json file.

Vaneet

From: Colin <col...@gm...>
Sent: April 8, 2025 1:00 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 config file

[△EXTERNAL]

Hi Vaneet
It will depend on your particular setup.

JBrowse 2 "likes" a single config.json, particularly because it enables comparing multiple genomes.

However, for either technical or administrative reasons, some people get overwhelmed by having a single config, and they make multiple configs

You can navigate to specific configs using

yoursite.com/jbrowse/?config=genomeA_config.json<http://yoursite.com/jbrowse/?config=genomeA_config.json>

You can also use the command line to write to specific configs using e.g.

jbrowse add-track --out genomeA_config.json

Finally, you can also optionally write scripts to merge configs. A script to merge configs tends to be pretty simple, you can simply concatenate the list of assemblies and tracks from different configs.


-Colin

PS We have had a couple great meetings with your XenBase colleagues!

On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I was curious when working with JBrowse2, is it very easy or user-friendly to setup multiple config.json files for the different genomes that may be hosted in the browser, similar to the original JBrowse?  If so, then please explain what the best way to do that is.  Or is JBrowse2 basically built to work best with one central config.json file as it is by default?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA


_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse2 config file

[Colin <col...@gm...>]

Hi Vaneet
It will depend on your particular setup.

JBrowse 2 "likes" a single config.json, particularly because it enables
comparing multiple genomes.

However, for either technical or administrative reasons, some people get
overwhelmed by having a single config, and they make multiple configs

You can navigate to specific configs using

yoursite.com/jbrowse/?config=genomeA_config.json

You can also use the command line to write to specific configs using e.g.

jbrowse add-track --out genomeA_config.json

Finally, you can also optionally write scripts to merge configs. A script
to merge configs tends to be pretty simple, you can simply concatenate the
list of assemblies and tracks from different configs.


-Colin

PS We have had a couple great meetings with your XenBase colleagues!

On Tue, Apr 8, 2025 at 11:59 AM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I was curious when working with JBrowse2, is it very easy or user-friendly
> to setup multiple config.json files for the different genomes that may be
> hosted in the browser, similar to the original JBrowse?  If so, then please
> explain what the best way to do that is.  Or is JBrowse2 basically built to
> work best with one central config.json file as it is by default?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 config file

[Vaneet L. <van...@uc...>]

Hello,

I was curious when working with JBrowse2, is it very easy or user-friendly to setup multiple config.json files for the different genomes that may be hosted in the browser, similar to the original JBrowse?  If so, then please explain what the best way to do that is.  Or is JBrowse2 basically built to work best with one central config.json file as it is by default?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

[Gmod-ajax] BOSC abstract deadline April 17

[Scott C. <sc...@sc...>]

]
Location: Liverpool, UK, and virtual
Dates: July 21-22, 2025
Website: https://www.open-bio.org/events/bosc/
LinkedIn: https://www.linkedin.com/groups/14344023/
Bluesky: https://bsky.app/profile/bosc.bsky.social
Slack:
https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew


Key Dates
April 17: Deadline for submitting talk/poster abstracts
<https://open-bio.org/events/bosc-2025/submit/>
May 13: Talk/poster acceptance notifications
May 15: Deadline for submitting late poster abstracts
July 20-24: ISMB/ECCB 2025 <https://www.iscb.org/ismbeccb2025/home>
July 21-22: BOSC 2025 <https://www.open-bio.org/events/bosc-2025/> (the
first two full days of ISMB/ECCB 2025)
July 22: BOSC/BOKR joint session
<https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/>
July 23-24: ISMB CollaborationFest
<https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/>

About BOSC: Since 2000, BOSC has provided a forum for sharing ideas and
results in open-source bioinformatics and open science. Our annual two-day
program includes keynote talks, talks chosen from submitted abstracts,
posters, a panel discussion, and more!

🍐BOSC NEWS 🍐
Joint session with BOKR: BOSC 2025 will include a joint session with the
newly renamed Bio-Ontologies and Knowledge Representation (BOKR) COSI
<https://www.open-bio.org/2025/03/17/BOSC-BOKR-2025/>! The joint session
will include talks chosen from abstracts submitted to BOSC or BOKR, plus a
keynote speaker who is well known in both the ontology and open science
communities (stay tuned for an announcement soon!).

Panel: Our panel topic this year will be Data Sustainability. A range of
experts will share their thoughts on this important and timely subject and
take questions from the audience.

ISMB CollaborationFest: This year, our popular collaborative work event (
CollaborationFest
<https://www.open-bio.org/events/bosc-2025/ismb-collaborationfest-2025/>,
aka CoFest) will be held as part of ISMB. Choose it as a free “add-on” when
you register for ISMB.

Submit an abstract!

Abstract submission is open until April 17 (end of the day Anywhere on
Earth - no extensions)! We encourage you to submit abstracts
<https://www.open-bio.org/events/bosc-2025/submit/> on any topic relevant
to open source bioinformatics or open science. After review, some abstracts
will be selected for lightning talks, longer talks, or posters.

Abstract submission is via ISMB’s EasyChair (linked from our submission page
<https://www.open-bio.org/events/bosc-2025/submit/>). Note that a short (<
250 words) text-only abstract is required for all submissions (talk or
poster), plus a “long abstract” (PDF, 2 pages max) if you want to be
considered for a talk.

BOSC topics include (but are not limited to):

   -

   Open Science and Reproducible Research
   -

   Open Biomedical Data
   -

   Citizen/Participatory Science
   -

   Standards and Interoperability
   -

   Data Science
   -

   Workflows
   -

   Translational Bioinformatics
   -

   Open Science
   -

   Developer Tools and Libraries
   -

   Outreach and Training
   -

   AI/ML: Open Approaches
   -

   Data Sustainability
   -

   Knowledge Representation and Ontologies (for joint session with BOKR)


Sponsors

We are thrilled to announce the first two sponsors
<https://www.open-bio.org/events/sponsors/> of BOSC 2025 (with more coming
soon)! Big thanks to these excellent organizations for supporting open
source bioinformatics and enabling us to offer free registration to some
qualified participants! 🎉

Platinum sponsor:

   <https://chanzuckerberg.com/>

The aim of CZI <https://chanzuckerberg.com/>’s Open Science program is the
universal and immediate open sharing of all scientific knowledge,
processes, and outputs.

Gold sponsor:
<https://seqera.io/>
Seqera <https://seqera.io/>, developed by the creators of Nextflow
<https://www.nextflow.io/>, empowers researchers to develop and deploy
scalable bioinformatics pipelines faster.


If your organization is interested in sponsoring BOSC, please let us know!
The more support we get, the more attendees we can offer financial
assistance to.

We hope to see you (in person in Liverpool or virtually) at BOSC 2025!

Sincerely,

BOSC 2025 Organizing Committee (Nomi Harris, Karsten Hokamp, Jessica Maia,
Hervé Ménager, Monica Munoz-Torres, Tazro Ohta, Deepak Unni, Jason Williams)



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                             Research Professor, Penn
State
Cite Us:

* The Galaxy Community. The Galaxy platform for accessible, reproducible,
and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024,
https://doi.org/10.1093/nar/gkae410

How to cite specific Galaxy instances and tools:
https://galaxyproject.org/citing-galaxy/

Re: [Gmod-ajax] Genomic Location Information File for Tracks on Flybase JBrowse

[Colin <col...@gm...>]

Hi there,
You might want to contact flybase

I was just looking around though and it looks like there are some downloads
for fly regulatory features via their wiki
https://wiki.flybase.org/wiki/FlyBase:JBrowse_Tracks#Genome_Level_Features

-Colin


On Fri, Mar 28, 2025 at 9:59 AM James Tan Sheng Yi <
jam...@tu...> wrote:

> To whom it may concern,
>
>
> Hi, I'd like to obtain the information for several tracks about genomic
> regulatory elements (e.g., enhancers, POL2 sites, etc.) on Flybase
> JBrowse. In particular, I need the genomic location information to
> answer questions of whether my set of interesting SNPs are enriched tend
> to fall within a particular type of genomic regulatory element (e.g.,
> enriched in enhancers of any type, enhancers of a specific type, TFBS,
> etc.). I have scoured the site and found no way of getting these genomic
> locations of each element in a track within a single file
> straightforwardly. Any help on how to do this?
>
> Thank you!
>
>
> Best,
>
> James
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Genomic Location Information File for Tracks on Flybase JBrowse

[James T. S. Yi <jam...@tu...>]

To whom it may concern,


Hi, I'd like to obtain the information for several tracks about genomic 
regulatory elements (e.g., enhancers, POL2 sites, etc.) on Flybase 
JBrowse. In particular, I need the genomic location information to 
answer questions of whether my set of interesting SNPs are enriched tend 
to fall within a particular type of genomic regulatory element (e.g., 
enriched in enhancers of any type, enhancers of a specific type, TFBS, 
etc.). I have scoured the site and found no way of getting these genomic 
locations of each element in a track within a single file 
straightforwardly. Any help on how to do this?

Thank you!


Best,

James

[Gmod-ajax] Apollo 2.8.0 released — Important Security Update

[Garrett S. <ste...@gm...>]

Version 2.8.0 of Apollo has been released:
https://github.com/GMOD/Apollo/releases/tag/2.8.0.

This release fixes security vulnerabilities in Apollo versions 2.4.0
through 2.7.0. For a detailed report of these vulnerabilities, please see
https://www.cisa.gov/news-events/ics-advisories/icsa-25-063-07.

In summary, the discovered vulnerabilities include the ability of a
malicious user to escalate their privileges within the Apollo app to admin
levels (that is, they can become an Apollo administrator), the ability to
retrieve a list of email addresses of other Apollo users, and - most
seriously of all - the ability to upload arbitrary files to the file system
in any directory writable by the Tomcat process that runs the Apollo
server. While the Tomcat documentation recommends not running Tomcat as the
root user, this advice is often ignored by Linux distributions; for
example, in Ubuntu, Tomcat runs as root. Consequently it seems likely that
many installations will face the worst-case scenario that a malicious user
could upload system files that would allow remote access to the Apollo
server.

*It is critical that you update your Apollo 2.4.0 to 2.7.0 installations as
soon as possible.* While we are not aware of any active exploitation of
these vulnerabilities, it is only a matter of time before publicly
disclosed vulnerabilities are systematically exploited by hackers.
Consequently, we strongly recommend applying the update to protect your
systems.

We also want to make it clear that these patches only apply to the legacy
2.0 version of Apollo. Since 2018, Apollo development has been folded into
the JBrowse project, and the recently released version of Apollo (v3.0) was
designed with security principles built in from the start. Naturally, as
maintainers of version 2.0, we take your system security extremely
seriously and have made every effort to provide this security update in as
timely a fashion as possible.

In addition to the aforementioned Apollo vulnerabilities, the CISA
researchers also discovered a reflected cross-site scripting (XSS)
vulnerability in JBrowse 1, and we have included a patch for this as well.
We also note that, as with the Apollo 2 flaws, these security flaws do not
apply to the latest version of JBrowse (JBrowse 2), which was designed with
stronger security patterns from the outset.

If you are using Docker to deploy Apollo, there are two different images
you can choose from. The gmod/apollo:release-2.8.0-alternate
<https://hub.docker.com/repository/docker/gmod/apollo/tags/release-2.8.0-alternate/sha256-a5d65e04fc597f0f71ea2c97dd6174ea1f1cca43912be53e3733c4fad2ee30e9>
image will provide a drop-in replacement for your existing Docker image.
This image, however, like past images, runs as the root user. If you would
like the additional security of not running as a root user, you can
use the gmod/apollo:release-2.8.0
image
<https://hub.docker.com/repository/docker/gmod/apollo/tags/release-2.8.0/sha256-9760d56c6ec28edc2d3793ed11e7e659da2a7ac1973f3b1cfa32517551c2ff46>,
which does not run as the root user, but will require you to update any
mounted directories so they are accessible by a non-root user.

We understand that updates are inconvenient, but we emphasize that taking
this proactive step is essential to ensuring the security of your systems.

Sincerely,

The Apollo Team