gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse2

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

Hi,

It was great to see this feature! I was looking forward to it from the
start of JBrowse2. Thanks to all the developers behind this! The URL works
well but the &sessionTracks didn't quite work for me so far, here is an
example:

http://myjbrowse2sites/testsite/?config=config.json&loc=1:6000-7000&assembly=Porcine%20S.%20scrofa%20v11.1&sessionTracks=[{"type":"FeatureTrack","trackId":"url_track","name":"URL
track","assemblyNames":["Porcine S. scrofa
v11.1"],"adapter":{"type":"FromConfigAdapter","features":[{"uniqueId":"one","refName":"1","start":6100,"end":6200,"name":"Boris"}]}}]

The url works properly up to the "sessionTracks" part, but there was no
dynamic track loaded or shown. Anyone have any advice? Do I need to code
the spaces in the configuration with "%20", too?

Thanks!

Ke

On Fri, Feb 4, 2022 at 11:45 AM han...@ge... <
han...@ge...> wrote:

> Hi Colin,
>     This is helpful for me. Thanks
>
> Best
>
> ------------------------------
> Hang Yang, Ph.D.
>
> Institute of Genetics and Developmental Biology
> Chinese Academy of Sciences
> No.1 West Beichen Road, Chaoyang District
> Beijing, China 100101
>
>
> *From:* Colin <col...@gm...>
> *Date:* 2022-02-03 05:25
> *To:* han...@ge...
> *CC:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse2
> Hi there
> JBrowse 1.6.4 merged this finally. Docs here
> https://jbrowse.org/jb2/docs/urlparams/
>
> Let me know if that helps:)
> -Colin
>
> On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
>
>> Hello,
>> This feature has been implemented on a work-in-progress branch. It is
>> planned to be released in an upcoming version soon
>>
>> https://github.com/GMOD/jbrowse-components/pull/2165
>>
>>
>> If you want to try to preview the feature before the official release you
>> can use the CLI command to test out the branch (it is otherwise up to date
>> with other latest release features)
>>
>>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>>
>> This will download the code from that branch to a folder named jbrowse2,
>> and then you can use URLs like
>>
>>
>> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>>
>>
>> -Colin
>>
>> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
>> han...@ge...> wrote:
>>
>>> Dear JBrowse developers,
>>>     I am a user of the JBrowse. It's really a useful tool.
>>>     I have a question about how to use URL query API in JBrowse2
>>>  e.g. specifying ?loc=1:1..100.
>>>     Thanks, Look forward to your reply.
>>>
>>> Best
>>>
>>> ------------------------------
>>> Hang Yang, Ph.D.
>>>
>>> Institute of Genetics and Developmental Biology
>>> Chinese Academy of Sciences
>>> No.1 West Beichen Road, Chaoyang District
>>> Beijing, China 100101
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse2

[<han...@ge...>]

Hi Colin,
    This is helpful for me. Thanks

Best



Hang Yang, Ph.D.

Institute of Genetics and Developmental Biology
Chinese Academy of Sciences
No.1 West Beichen Road, Chaoyang District
Beijing, China 100101
 
From: Colin
Date: 2022-02-03 05:25
To: han...@ge...
CC: gmod-ajax
Subject: Re: [Gmod-ajax] JBrowse2
Hi there
JBrowse 1.6.4 merged this finally. Docs here https://jbrowse.org/jb2/docs/urlparams/ 

Let me know if that helps:)
-Colin

On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:
Hello,
This feature has been implemented on a work-in-progress branch. It is planned to be released in an upcoming version soon

https://github.com/GMOD/jbrowse-components/pull/2165


If you want to try to preview the feature before the official release you can use the CLI command to test out the branch (it is otherwise up to date with other latest release features)

    jbrowse create --branch nav_with_urlbar2 jbrowse2

This will download the code from that branch to a folder named jbrowse2, and then you can use URLs like

http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2


-Colin

On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <han...@ge...> wrote:
Dear JBrowse developers,
    I am a user of the JBrowse. It's really a useful tool. 
    I have a question about how to use URL query API in JBrowse2 e.g. specifying ?loc=1:1..100. 
    Thanks, Look forward to your reply.
    
Best



Hang Yang, Ph.D.

Institute of Genetics and Developmental Biology
Chinese Academy of Sciences
No.1 West Beichen Road, Chaoyang District
Beijing, China 100101
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse genome assemble setup issues

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

Hi there Charan!
I am sorry I missed this email awhile back. Were you able to resolve?


Generally, you use add-assembly command before add-track. The add-assembly
will create the config.json

Interested to see if there is a way to think about your S3 deployment. If
you wanted to use GUI admin server and an s3 bucket, I would develop it
locally, and then upload to S3 after you are finished

Note: Our JBrowse instance e.g. at https://jbrowse.org/code/jb2/v1.6.4 is
on an S3 bucket.

-Colin

On Mon, Sep 20, 2021 at 11:01 AM Charan Thoomu <
Cha...@eg...> wrote:

> Hi,
>
>
>
> All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we
> don't want to make our S3 bucket Public for security purposes.
>
>
>
> I tried both GUI and CLI approaches for adding the files, I have doubts in
> both the approaches as follows:
>
>
>
> Approach 1: GUI
>
> While creating a new Genome Assembly, it is expecting only an URL , in our
> case even if I give the S3 URL, it won't be able to fetch it because S3's
> public access is blocked.
>
>
>
> Is there an alternative way to create Genome Assembly without providing an
> URL, instead adding from the EC2 instance is preferred?
>
>
>
>
>
>
>
>
>
> Approach 2: CLI
>
> 1.    Can I add tracks without adding assembly?
>
> 2.    I tried running " jbrowse add - track / data /*****.fa -- load
> copy" for adding tracks but I encountered -
>
> "    Error: ENOENT: no such file or directory, open './config.json'
>
>     Code: ENOENT
>     Try this:
>       * Make sure the file "./config.json" exists
>       * Run `jbrowse add-assembly` to create a config file
>
> "
>
> ·  If I have to run the 'jbrowse add-assembly /data/*****.fa  --load copy'
> command, should I be in any specific directory to pick up the file? I am
> asking because when I run this command I am getting: " Error: Could not
> resolve to a file or a URL: " What am I missing here?
>
> Please help me with detailed information.
>
>
>
> --
>
> Thanks,
>
> Charan
>
>
>
>
>
> Charan Thoomu
>
> Software Engineer
>
> eGenesis, Inc.
>
> 300 Technology Square, Suite 301
>
> Cambridge, MA 02139
>
> cha...@eg...
>
> www.egenesisbio.com
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse2

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

Hi there
JBrowse 1.6.4 merged this finally. Docs here
https://jbrowse.org/jb2/docs/urlparams/

Let me know if that helps:)
-Colin

On Tue, Jan 11, 2022 at 11:02 AM Colin <col...@gm...> wrote:

> Hello,
> This feature has been implemented on a work-in-progress branch. It is
> planned to be released in an upcoming version soon
>
> https://github.com/GMOD/jbrowse-components/pull/2165
>
>
> If you want to try to preview the feature before the official release you
> can use the CLI command to test out the branch (it is otherwise up to date
> with other latest release features)
>
>     jbrowse create --branch nav_with_urlbar2 jbrowse2
>
> This will download the code from that branch to a folder named jbrowse2,
> and then you can use URLs like
>
>
> http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2
>
>
> -Colin
>
> On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
> han...@ge...> wrote:
>
>> Dear JBrowse developers,
>>     I am a user of the JBrowse. It's really a useful tool.
>>     I have a question about how to use URL query API in JBrowse2
>>  e.g. specifying ?loc=1:1..100.
>>     Thanks, Look forward to your reply.
>>
>> Best
>>
>> ------------------------------
>> Hang Yang, Ph.D.
>>
>> Institute of Genetics and Developmental Biology
>> Chinese Academy of Sciences
>> No.1 West Beichen Road, Chaoyang District
>> Beijing, China 100101
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] jbrowse2 searching question

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

Hi there
JBrowse 1.6.4 finally added the URL parameter API. See
https://jbrowse.org/jb2/docs/urlparams/ !

Let me know if that helps:)
-Colin

On Fri, Nov 26, 2021 at 12:34 PM Colin <col...@gm...> wrote:

> Hi there,
> JBrowse 2 doesn't yet have the ability to navigate using the URL bar, but
> you can perform e.g. searches with locstrings or gene names inside the user
> interface if you have run `jbrowse text-index` on your config
>
> We are working on adding navigation to the URL bar e.g. adding
> ?loc=chr1:100-200 to the URL to navigate here
> https://github.com/GMOD/jbrowse-components/pull/2165 and it is hopefully
> near completion
>
> -Colin
>
> On Fri, Nov 26, 2021 at 1:53 PM ren...@no... <
> ren...@no...> wrote:
>
>>
>> Hello:
>>
>> Ask a question about jBrowse2 search. Jbrowse1 can jump to the
>> corresponding gene by typing location information into the address bar, but
>> jBrowse2 doesn't work.Is it disabled?Or change the new search form?Thank
>> you for your information!
>>
>> Best wishes！
>> ------------------------------
>> ren...@no...
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse installation failed (node_modules dir not found)

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

you will likely need to use an older node version, version 14 or less (your
log says you are using node 17). this is a known issue that is mentioned in
the README

the readme note says

Note: if you are using plugins with a dev version of JBrowse or installing
from GitHub, you may need to use node <=14 (e.g. node >=15 may fail) due to
node-sass not compiling on newer node versions easily. See
https://github.com/GMOD/jbrowse/pull/1607 for details


-Colin


On Fri, Jan 21, 2022 at 12:14 AM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
> I'm trying to install JBrowse on a new Ubuntu server for the first time.
> I have been following the instructions on the JBrowse 1 documentation page
> and I installed Node.js accordingly beforehand.  I wanted a release for
> which I can make changes and add plugins so I used 'git clone' and checked
> out the latest release as it was indicated.  After running ./setup.sh, I
> get errors that start with looking for files in a node_modules folder which
> does not exist in my JBrowse release:
>
> 7612 error code 1
> 7613 error path
> /var/www/html/JBrowse-1.16.11-release/node_modules/node-sass
> 7614 error command failed
> 7615 error command sh -c node scripts/build.js
> 7616 error Building: /usr/bin/node
> /var/www/html/JBrowse-1.16.11-release/node_modules/node-gyp/bin/node-gyp.js
> rebuild --verbose --libsass_ext= --libsass_cflags= --libsass_ldflags=
> --libsass_library=
> 7616 error make: Entering directory
> '/var/www/html/JBrowse-1.16.11-release/node_modules/node-sass/build'
> ....
>
> I attached the full log.  Is the node_modules folder supposed to be there
> in the release?  I also installed python2 as there were some errors earlier
> that indicated it was needed.  Please let me know how this can be resolved
> to install JBrowse.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse installation failed (node_modules dir not found)

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

Hello,

I'm trying to install JBrowse on a new Ubuntu server for the first time.  I have been following the instructions on the JBrowse 1 documentation page and I installed Node.js accordingly beforehand.  I wanted a release for which I can make changes and add plugins so I used 'git clone' and checked out the latest release as it was indicated.  After running ./setup.sh, I get errors that start with looking for files in a node_modules folder which does not exist in my JBrowse release:

7612 error code 1
7613 error path /var/www/html/JBrowse-1.16.11-release/node_modules/node-sass
7614 error command failed
7615 error command sh -c node scripts/build.js
7616 error Building: /usr/bin/node /var/www/html/JBrowse-1.16.11-release/node_modules/node-gyp/bin/node-gyp.js rebuild --verbose --libsass_ext= --libsass_cflags= --libsass_ldflags= --libsass_library=
7616 error make: Entering directory '/var/www/html/JBrowse-1.16.11-release/node_modules/node-sass/build'
....

I attached the full log.  Is the node_modules folder supposed to be there in the release?  I also installed python2 as there were some errors earlier that indicated it was needed.  Please let me know how this can be resolved to install JBrowse.

Thanks,

Vaneet

Re: [Gmod-ajax] Regarding JBrowse

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

Hello Uday,

For 1, you can add multiple tracks inside the "tracks" array. You can see
one of our example configs here:
https://github.com/GMOD/jbrowse-components/blob/d95dc2cc595c51bbfd7ed363b5e7c2b6b48a0eaa/test_data/volvox/config.json#L88-L127
.

For 2, what specification of GFF is your file using? We support GFF3, and
if you have GFF2 you might be able to get it to work using the GTF adapter
type. Another thing to check is that your reference sequence names match.
>From your screenshot it looks like your reference sequence file uses the
name "chr_001". Does this match the name in your GFF file? If not, you will
need to either change the names to match or set up reference name aliasing
<https://jbrowse.org/jb2/docs/config_guide/#configuring-reference-name-aliasing>
.

Best,
Garrett

On Thu, Jan 13, 2022 at 8:49 AM Uday Sai Reddy Ambati via Gmod-ajax <
gmo...@li...> wrote:

> Hello,
>
> I have a few questions regarding JBrowse. Can you please help me
>
> 1) I am attaching a screenshot of the configuration file, Is there any way
> that I can  add multiple tracks to the config file so that I can select any
> of the tracks that I want, If so please let me know how to do it.
>
> 2) I am trying to add a gff file type, not a gff3 type to the config file,
> but I cannot see anything regarding that on the screen. I am attaching a
> screenshot of that too. Is there anything wrong with this file type?
>
> Please let me know the solution for these issues. Thank you for your time.
>
> Thank you,
> Uday Ambati.
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Regarding JBrowse

[Uday S. R. A. <ua...@ma...>]

Hello,

I have a few questions regarding JBrowse. Can you please help me

1) I am attaching a screenshot of the configuration file, Is there any way
that I can  add multiple tracks to the config file so that I can select any
of the tracks that I want, If so please let me know how to do it.

2) I am trying to add a gff file type, not a gff3 type to the config file,
but I cannot see anything regarding that on the screen. I am attaching a
screenshot of that too. Is there anything wrong with this file type?

Please let me know the solution for these issues. Thank you for your time.

Thank you,
Uday Ambati.

Re: [Gmod-ajax] JBrowse2

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

Hello,
This feature has been implemented on a work-in-progress branch. It is
planned to be released in an upcoming version soon

https://github.com/GMOD/jbrowse-components/pull/2165


If you want to try to preview the feature before the official release you
can use the CLI command to test out the branch (it is otherwise up to date
with other latest release features)

    jbrowse create --branch nav_with_urlbar2 jbrowse2

This will download the code from that branch to a folder named jbrowse2,
and then you can use URLs like

http://yoursite.com/jbrowse2/?loc=chr1:1-100&assembly=hg19&tracks=track_id1,track_id2


-Colin

On Tue, Jan 11, 2022 at 10:12 AM han...@ge... <
han...@ge...> wrote:

> Dear JBrowse developers,
>     I am a user of the JBrowse. It's really a useful tool.
>     I have a question about how to use URL query API in JBrowse2
>  e.g. specifying ?loc=1:1..100.
>     Thanks, Look forward to your reply.
>
> Best
>
> ------------------------------
> Hang Yang, Ph.D.
>
> Institute of Genetics and Developmental Biology
> Chinese Academy of Sciences
> No.1 West Beichen Road, Chaoyang District
> Beijing, China 100101
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2

[<han...@ge...>]

Dear JBrowse developers,
    I am a user of the JBrowse. It's really a useful tool. 
    I have a question about how to use URL query API in JBrowse2 e.g. specifying ?loc=1:1..100. 
    Thanks, Look forward to your reply.
    
Best



Hang Yang, Ph.D.

Institute of Genetics and Developmental Biology
Chinese Academy of Sciences
No.1 West Beichen Road, Chaoyang District
Beijing, China 100101

Re: [Gmod-ajax] JBrowse - log4js vulnerability

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

Hi there
I am aware of the log4j issue but this particular warning is not really a
concern in my opinion. To put this in perspective, jbrowse does not have
any server side code that "runs", it is just a set of js css and html e.g.
static resources, so this log4j code is not "running" anywhere on your
machine

-Colin

On Tue, Jan 4, 2022, 10:11 AM Istvan Nagy <ist...@qg...> wrote:

> Hi All,
>
> I am running a public genome browser with runnin It appears that
> jbrowse-1.16.10.
>
> It appears the JBrowse has log4j security issue:
>
>
> ===============================================================================
>
> [WARNING] [42 - contains log4j files]
> /usr/local/jbrowse/node_modules/dojo-util/buildscripts/cldr/lib/bsf.jar
> [WARNING] [43 - contains log4j files]
>
> /usr/local/jbrowse/node_modules/dojo-util/buildscripts/cldr/lib/commons-logging-1.1.1.jar
> [WARNING] [55 - contains log4j files]
>
> /usr/local/jbrowse-1.16.10-release/node_modules/dojo-util/buildscripts/cldr/lib/bsf.jar
> [WARNING] [56 - contains log4j files]
>
> /usr/local/jbrowse-1.16.10-release/node_modules/dojo-util/buildscripts/cldr/lib/commons-logging-1.1.1.jar
> [WARNING] This script does not guarantee that you are not vulnerable,
> but is a strong hint.
> ==============================================================================
>
>
>
> I am wondering whether a security update for JBrowse 1.x is planned in
> the near future ?
>
>
> Thanks
>
> Istvan
>
> --
> Med venlig hilsen / Kind regards
> Istvan Nagy
>
> Center for Quantitative Genetics and Genomics
> AARHUS UNIVERSITET / AARHUS UNIVERSITY
> Forsøgsvej 1
> DK-4200 Slagelse, Denmark
> Tel: +45 8715 6000
> Email: ist...@qg...
> +45 8715 8208 (direct)
> Web: http://www.au.dk
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse - log4js vulnerability

[Istvan N. <ist...@qg...>]

Hi All,

I am running a public genome browser with runnin It appears that 
jbrowse-1.16.10.

It appears the JBrowse has log4j security issue:

===============================================================================

[WARNING] [42 - contains log4j files] 
/usr/local/jbrowse/node_modules/dojo-util/buildscripts/cldr/lib/bsf.jar
[WARNING] [43 - contains log4j files] 
/usr/local/jbrowse/node_modules/dojo-util/buildscripts/cldr/lib/commons-logging-1.1.1.jar
[WARNING] [55 - contains log4j files] 
/usr/local/jbrowse-1.16.10-release/node_modules/dojo-util/buildscripts/cldr/lib/bsf.jar
[WARNING] [56 - contains log4j files] 
/usr/local/jbrowse-1.16.10-release/node_modules/dojo-util/buildscripts/cldr/lib/commons-logging-1.1.1.jar
[WARNING] This script does not guarantee that you are not vulnerable, 
but is a strong hint.
============================================================================== 


I am wondering whether a security update for JBrowse 1.x is planned in 
the near future ?


Thanks

Istvan

-- 
Med venlig hilsen / Kind regards
Istvan Nagy

Center for Quantitative Genetics and Genomics
AARHUS UNIVERSITET / AARHUS UNIVERSITY
Forsøgsvej 1
DK-4200 Slagelse, Denmark
Tel: +45 8715 6000
Email: ist...@qg...
+45 8715 8208 (direct)
Web: http://www.au.dk

Re: [Gmod-ajax] Regarding JBrowse

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

Hi Uday,

For your (2), you can change the color by adding some configuration to your
config.json. That particular color is the "secondary" one. You can see some
examples here:
https://jbrowse.org/jb2/docs/config_guide/#configuring-the-theme

For (1), I'm not sure if there's an easy way to do that. There aren't any
existing examples that I know of, so I'll have to think a bit more.

Best regards,
Garrett


On Sat, Dec 18, 2021 at 9:28 PM Uday Sai Reddy Ambati via Gmod-ajax <
gmo...@li...> wrote:

> Hello,
>
> Hope you are doing well. I am Uday Ambati.I have a few questions regarding
> JBrowse.
>
> 1) Is there any way to add a web link in the right side part of the screen
> that is below the Available tracks?
>
> 2) Is there any way to change the background ground color on the Available
> tracks, i.e, from violet to some other color?
>
> I am attaching a screenshot and some text fields on it to let you
> understand what those changes that I am talking about.
>
> If there are any solutions, Can you please let me know how to do them.
>
> Thanks & Regards,
> Uday Ambati.
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Regarding JBrowse

[Uday S. R. A. <ua...@ma...>]

Hello,

Hope you are doing well. I am Uday Ambati.I have a few questions regarding
JBrowse.

1) Is there any way to add a web link in the right side part of the screen
that is below the Available tracks?

2) Is there any way to change the background ground color on the Available
tracks, i.e, from violet to some other color?

I am attaching a screenshot and some text fields on it to let you
understand what those changes that I am talking about.

If there are any solutions, Can you please let me know how to do them.

Thanks & Regards,
Uday Ambati.

Re: [Gmod-ajax] jbrowse2 searching question

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

Hi there,
JBrowse 2 doesn't yet have the ability to navigate using the URL bar, but
you can perform e.g. searches with locstrings or gene names inside the user
interface if you have run `jbrowse text-index` on your config

We are working on adding navigation to the URL bar e.g. adding
?loc=chr1:100-200 to the URL to navigate here
https://github.com/GMOD/jbrowse-components/pull/2165 and it is hopefully
near completion

-Colin

On Fri, Nov 26, 2021 at 1:53 PM ren...@no... <
ren...@no...> wrote:

>
> Hello:
>
> Ask a question about jBrowse2 search. Jbrowse1 can jump to the
> corresponding gene by typing location information into the address bar, but
> jBrowse2 doesn't work.Is it disabled?Or change the new search form?Thank
> you for your information!
>
> Best wishes！
> ------------------------------
> ren...@no...
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] jbrowse2 searching question

[<ren...@no...>]

Hello:
Ask a question about jBrowse2 search. Jbrowse1 can jump to the corresponding gene by typing location information into the address bar, but jBrowse2 doesn't work.Is it disabled?Or change the new search form?Thank you for your information!
Best wishes！


ren...@no...

Re: [Gmod-ajax] JBrowse issue

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

Hi there,
I think all that is needed is to zoom in closer and you will, for example,
see the DNA letters of the FASTA file. Is there something different you are
interested in seeing?

-Colin

On Tue, Nov 23, 2021 at 12:36 PM Uday Sai Reddy Ambati via Gmod-ajax <
gmo...@li...> wrote:

> Hello,
>
> I am trying to run JBrowse. I am able to display the gff3 file, but I am
> not able to do the same with the fasta assembly file. So Can you please
> suggest to me what to do in order to display the assembly file. I am
> attaching a screenshot of it.
>
> Thank you,
> Uday Ambati.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse issue

[Uday S. R. A. <ua...@ma...>]

Hello,

I am trying to run JBrowse. I am able to display the gff3 file, but I am
not able to do the same with the fasta assembly file. So Can you please
suggest to me what to do in order to display the assembly file. I am
attaching a screenshot of it.

Thank you,
Uday Ambati.

Re: [Gmod-ajax] GFF3 slow loading with JBrowse2

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

I never thought this could be region specific. Maybe I'll do more tests
with more regions, so far I've only used a limited number of regions. Could
this also be some problems on the client/browser side, such as too much
memory used by Firefox/Chrome?

Thanks for all the extra info about rendering GFF3. They are really helpful
for me to consider ways to optimize GFF3s for JBrowse2. Really appreciate
it

Ke

On Mon, Nov 22, 2021 at 3:06 PM Colin <col...@gm...> wrote:

> Do you have an example of a region that is slow to load?
>
> The mRNA features would need child feature resolution
>
> The scaffold features would not, and could be added to the dontRedispatch
> list (we could add it to the default list too)
>
> -Colin
>
> On Mon, Nov 22, 2021 at 3:36 PM Ke Jiang <bio...@gm...> wrote:
>
>> Thanks for the info! I took one GFF3, directly coming from Ensembl, and
>> did some digging: the only feature covering the entire chromosomes are
>> "chromosome" features, which should not affect the child feature
>> resolution. But there are about 100 "mRNA" and "scaffold" features that are
>> larger than 1Mbp. They would need full resolution of child features. Would
>> these affect the loading speed?
>>
>> Here is the GFF3 file used, if some tests need to be run:
>>
>> http://ftp.ensembl.org/pub/release-99/gff3/sus_scrofa/
>>
>> The last one in the list called "Sus_scrofa.Sscrofa11.1.99.gff3.gz"
>>
>>
>> On Mon, Nov 22, 2021 at 2:18 PM Colin <col...@gm...> wrote:
>>
>>> One common reason for slowness is if you have features that cover the
>>> entire chromosome for gff3
>>>
>>> The mechanisms of the gff3tabix make it try to resolve all the child
>>> features of large parent features, but if it's e.g. a "region" feature (col
>>> 3 says region) that covers the entirety of chr1, then jbrowse doesn't need
>>> to resolve the child features for that object. By default, region,
>>> chromosome, and contig type gff3 features don't perform this, but if you
>>> have a different type of gff3 feature that covers the entirety of of your
>>> chromosomes, then maybe you can either rename that type to "region" or add
>>> to the "dontRedispatch" config slot on the Gff3TabixAdapter
>>>
>>> -Colin
>>>
>>> On Mon, Nov 22, 2021 at 2:33 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I've been playing with JBrowse2 for a while. Recently I noticed that
>>>> GFF3 files, while following the instructions of gt sorting, bgzipping, and
>>>> tabix indexing, still load very slowly on JBrowse2 even for a very small
>>>> genomic interval. An interval as small as 100bp could take up to 5min to
>>>> load. This seems to only happen to those genome-wide GFF3 files such as
>>>> genome annotations and GFFs from StringTie or TopHat pipelines. A BED file
>>>> with a few entries loads very fast when zipped and indexed. BAMs/BigWigs
>>>> also load pretty fast. Does anyone also have this problem or notice similar
>>>> behaviors of large GFF3 files? All files are not stored locally on the
>>>> JBrowse2 server but stay in an S3 bucket on another server, if this
>>>> information helps.
>>>>
>>>> Thanks!
>>>>
>>>> Ke
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>

Re: [Gmod-ajax] GFF3 slow loading with JBrowse2

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

Do you have an example of a region that is slow to load?

The mRNA features would need child feature resolution

The scaffold features would not, and could be added to the dontRedispatch
list (we could add it to the default list too)

-Colin

On Mon, Nov 22, 2021 at 3:36 PM Ke Jiang <bio...@gm...> wrote:

> Thanks for the info! I took one GFF3, directly coming from Ensembl, and
> did some digging: the only feature covering the entire chromosomes are
> "chromosome" features, which should not affect the child feature
> resolution. But there are about 100 "mRNA" and "scaffold" features that are
> larger than 1Mbp. They would need full resolution of child features. Would
> these affect the loading speed?
>
> Here is the GFF3 file used, if some tests need to be run:
>
> http://ftp.ensembl.org/pub/release-99/gff3/sus_scrofa/
>
> The last one in the list called "Sus_scrofa.Sscrofa11.1.99.gff3.gz"
>
>
> On Mon, Nov 22, 2021 at 2:18 PM Colin <col...@gm...> wrote:
>
>> One common reason for slowness is if you have features that cover the
>> entire chromosome for gff3
>>
>> The mechanisms of the gff3tabix make it try to resolve all the child
>> features of large parent features, but if it's e.g. a "region" feature (col
>> 3 says region) that covers the entirety of chr1, then jbrowse doesn't need
>> to resolve the child features for that object. By default, region,
>> chromosome, and contig type gff3 features don't perform this, but if you
>> have a different type of gff3 feature that covers the entirety of of your
>> chromosomes, then maybe you can either rename that type to "region" or add
>> to the "dontRedispatch" config slot on the Gff3TabixAdapter
>>
>> -Colin
>>
>> On Mon, Nov 22, 2021 at 2:33 PM Ke Jiang <bio...@gm...> wrote:
>>
>>> Hi,
>>>
>>> I've been playing with JBrowse2 for a while. Recently I noticed that
>>> GFF3 files, while following the instructions of gt sorting, bgzipping, and
>>> tabix indexing, still load very slowly on JBrowse2 even for a very small
>>> genomic interval. An interval as small as 100bp could take up to 5min to
>>> load. This seems to only happen to those genome-wide GFF3 files such as
>>> genome annotations and GFFs from StringTie or TopHat pipelines. A BED file
>>> with a few entries loads very fast when zipped and indexed. BAMs/BigWigs
>>> also load pretty fast. Does anyone also have this problem or notice similar
>>> behaviors of large GFF3 files? All files are not stored locally on the
>>> JBrowse2 server but stay in an S3 bucket on another server, if this
>>> information helps.
>>>
>>> Thanks!
>>>
>>> Ke
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] GFF3 slow loading with JBrowse2

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

Thanks for the info! I took one GFF3, directly coming from Ensembl, and did
some digging: the only feature covering the entire chromosomes are
"chromosome" features, which should not affect the child feature
resolution. But there are about 100 "mRNA" and "scaffold" features that are
larger than 1Mbp. They would need full resolution of child features. Would
these affect the loading speed?

Here is the GFF3 file used, if some tests need to be run:

http://ftp.ensembl.org/pub/release-99/gff3/sus_scrofa/

The last one in the list called "Sus_scrofa.Sscrofa11.1.99.gff3.gz"


On Mon, Nov 22, 2021 at 2:18 PM Colin <col...@gm...> wrote:

> One common reason for slowness is if you have features that cover the
> entire chromosome for gff3
>
> The mechanisms of the gff3tabix make it try to resolve all the child
> features of large parent features, but if it's e.g. a "region" feature (col
> 3 says region) that covers the entirety of chr1, then jbrowse doesn't need
> to resolve the child features for that object. By default, region,
> chromosome, and contig type gff3 features don't perform this, but if you
> have a different type of gff3 feature that covers the entirety of of your
> chromosomes, then maybe you can either rename that type to "region" or add
> to the "dontRedispatch" config slot on the Gff3TabixAdapter
>
> -Colin
>
> On Mon, Nov 22, 2021 at 2:33 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I've been playing with JBrowse2 for a while. Recently I noticed that GFF3
>> files, while following the instructions of gt sorting, bgzipping, and tabix
>> indexing, still load very slowly on JBrowse2 even for a very small genomic
>> interval. An interval as small as 100bp could take up to 5min to load. This
>> seems to only happen to those genome-wide GFF3 files such as genome
>> annotations and GFFs from StringTie or TopHat pipelines. A BED file with a
>> few entries loads very fast when zipped and indexed. BAMs/BigWigs also load
>> pretty fast. Does anyone also have this problem or notice similar behaviors
>> of large GFF3 files? All files are not stored locally on the JBrowse2
>> server but stay in an S3 bucket on another server, if this information
>> helps.
>>
>> Thanks!
>>
>> Ke
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] GFF3 slow loading with JBrowse2

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

If you think this doesn't apply to you, feel free to send us the GFF in
question and we can check it out, can send to my email or to mailing list

-Colin

On Mon, Nov 22, 2021 at 3:17 PM Colin <col...@gm...> wrote:

> One common reason for slowness is if you have features that cover the
> entire chromosome for gff3
>
> The mechanisms of the gff3tabix make it try to resolve all the child
> features of large parent features, but if it's e.g. a "region" feature (col
> 3 says region) that covers the entirety of chr1, then jbrowse doesn't need
> to resolve the child features for that object. By default, region,
> chromosome, and contig type gff3 features don't perform this, but if you
> have a different type of gff3 feature that covers the entirety of of your
> chromosomes, then maybe you can either rename that type to "region" or add
> to the "dontRedispatch" config slot on the Gff3TabixAdapter
>
> -Colin
>
> On Mon, Nov 22, 2021 at 2:33 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I've been playing with JBrowse2 for a while. Recently I noticed that GFF3
>> files, while following the instructions of gt sorting, bgzipping, and tabix
>> indexing, still load very slowly on JBrowse2 even for a very small genomic
>> interval. An interval as small as 100bp could take up to 5min to load. This
>> seems to only happen to those genome-wide GFF3 files such as genome
>> annotations and GFFs from StringTie or TopHat pipelines. A BED file with a
>> few entries loads very fast when zipped and indexed. BAMs/BigWigs also load
>> pretty fast. Does anyone also have this problem or notice similar behaviors
>> of large GFF3 files? All files are not stored locally on the JBrowse2
>> server but stay in an S3 bucket on another server, if this information
>> helps.
>>
>> Thanks!
>>
>> Ke
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] GFF3 slow loading with JBrowse2

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

One common reason for slowness is if you have features that cover the
entire chromosome for gff3

The mechanisms of the gff3tabix make it try to resolve all the child
features of large parent features, but if it's e.g. a "region" feature (col
3 says region) that covers the entirety of chr1, then jbrowse doesn't need
to resolve the child features for that object. By default, region,
chromosome, and contig type gff3 features don't perform this, but if you
have a different type of gff3 feature that covers the entirety of of your
chromosomes, then maybe you can either rename that type to "region" or add
to the "dontRedispatch" config slot on the Gff3TabixAdapter

-Colin

On Mon, Nov 22, 2021 at 2:33 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I've been playing with JBrowse2 for a while. Recently I noticed that GFF3
> files, while following the instructions of gt sorting, bgzipping, and tabix
> indexing, still load very slowly on JBrowse2 even for a very small genomic
> interval. An interval as small as 100bp could take up to 5min to load. This
> seems to only happen to those genome-wide GFF3 files such as genome
> annotations and GFFs from StringTie or TopHat pipelines. A BED file with a
> few entries loads very fast when zipped and indexed. BAMs/BigWigs also load
> pretty fast. Does anyone also have this problem or notice similar behaviors
> of large GFF3 files? All files are not stored locally on the JBrowse2
> server but stay in an S3 bucket on another server, if this information
> helps.
>
> Thanks!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] GFF3 slow loading with JBrowse2

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

Hi,

I've been playing with JBrowse2 for a while. Recently I noticed that GFF3
files, while following the instructions of gt sorting, bgzipping, and tabix
indexing, still load very slowly on JBrowse2 even for a very small genomic
interval. An interval as small as 100bp could take up to 5min to load. This
seems to only happen to those genome-wide GFF3 files such as genome
annotations and GFFs from StringTie or TopHat pipelines. A BED file with a
few entries loads very fast when zipped and indexed. BAMs/BigWigs also load
pretty fast. Does anyone also have this problem or notice similar behaviors
of large GFF3 files? All files are not stored locally on the JBrowse2
server but stay in an S3 bucket on another server, if this information
helps.

Thanks!

Ke