gmod-ajax — JBrowse list

Re: [Gmod-ajax] Organization of multiple samples in subfolders

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

Hi Ahmet,

Let me start with this: display and data storage are completely separate;
you can have all of the data in a single directory if you want, and still
have them display organized by lab or dataset (though of course, it might
make life easier for you if you have them mirror each other).  But the
point is, if you have them laid out one way in the display and decide it
doesn't work well for your users, you can change the display without having
to change the underlying file system.  I imagine this flexibility is at the
root of your observation that documentation are not clear in what you want
to know.

I suppose what I would do if I were setting this up would be to create
dataset directories where the files are stored, plus a json file that
defines the tracks associated with that dataset. Then in the main
trackList.json file, you can use include directives to pull in all of the
configurations for the different datasets. The only possible downside to
this is that it will require several "extra" http GETs to fetch each of the
include files.  Depending on how many include files you have, it might be a
noticeable slowdown on initial startup.  If that happens, you could write a
little script that combines all of the include files into a single
trackList.json for your production site.  I do that for the main C. elegans
JBrowse instance at WormBase because I would have to do includes for about
70 files, causing the load time to go up by 5 or 10 seconds.  The other
species at WormBase though just use the includes because they have
significantly fewer tracks.  The script that does the "bundling" of the
various include files is here:

https://github.com/WormBase/website-genome-browsers/blob/jbrowse-staging/jbrowse/bin/bundle_track_config.pl

A trackList.json file that uses includes looks like this:

https://www.wormbase.org/tools/genome/jbrowse-simple/data/b_malayi_PRJNA10729/trackList.json

and an include file looks like this:

https://www.wormbase.org/tools/genome/jbrowse-simple/data/b_malayi_PRJNA10729/includes/genes.json

(on a side note--this is one of the things that I really love about
JBrowse: the configuration files for public sites are easily viewable, so
if you find a display you really like, you can look at how they did it.)

Finally, to group the tracks together by dataset, you can make use of the
"category" attribute and the default hierarchical track selector (
http://jbrowse.org/docs/track_selectors.html).  You can also make
subcategories by including a forward slash in the name of the category,
which will result in a "sub-box" in the track selector.

Ok, that's enough to get you started :-) Please let us know if you have
more questions.

Scott




On Fri, Aug 16, 2019 at 10:44 AM Ozturk, Ahmet <Ahm...@um...>
wrote:

> Hello,
>
> I’m trying to set up JBrowse for the data in our lab for around 200
> samples. I’m working on the documentation, however, some parts are not
> clear and I have some questions about the organization of data and conf
> files. What is the best practice for adding many tracks, grouped by
> researchers or datasets? I want people in the lab to compare their data to
> others. Is it a good practice to create folders for each researcher, and
> subfolders for each dataset containing 2 or more bam files and create
> subcategories in the main conf file? Also, is there a way to create
> individual conf files for each dataset/subfolder and include those in the
> main conf file so that it’s tidy and easy to maintain?
>
> Thanks, Best,
>
>
> Ahmet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Organization of multiple samples in subfolders

[Ozturk, A. <Ahm...@um...>]

Hello,

I’m trying to set up JBrowse for the data in our lab for around 200 samples. I’m working on the documentation, however, some parts are not clear and I have some questions about the organization of data and conf files. What is the best practice for adding many tracks, grouped by researchers or datasets? I want people in the lab to compare their data to others. Is it a good practice to create folders for each researcher, and subfolders for each dataset containing 2 or more bam files and create subcategories in the main conf file? Also, is there a way to create individual conf files for each dataset/subfolder and include those in the main conf file so that it’s tidy and easy to maintain?

Thanks, Best,


Ahmet

Re: [Gmod-ajax] jBrowse set up issue

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

Hi Chin-Rang,

That's good news--the only downside to using the non-dev version is that
you can't install plugins if there are any you want--but that's a problem
for another day :-)

Scott


On Tue, Aug 13, 2019 at 11:55 AM Yang, Chin-Rang (NIH/NHLBI) [E] <
chi...@ni...> wrote:

> Yes, it is working now with non-dev version.
>
> Thank you very much.
>
>
>
> Chin-Rang
>
>
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Tuesday, August 13, 2019 2:26 PM
> *To:* Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
> *Subject:* Re: [Gmod-ajax] jBrowse set up issue
>
>
>
> Hi Chin-Rang,
>
>
>
> The trick with sorting out a 404 error is to examine the url it's trying
> to fetch and then figure out why the file it's looking for isn't where it
> expects.  If you have jbrowse-dev, you'll need to run setup.sh (oh, which
> probably won't work on Windows) to generate the javascript bundle files.  I
> believe if you get the non-dev version, those files are already generated.
>
>
>
> Scott
>
>
>
>
>
> On Tue, Aug 13, 2019 at 11:24 AM Scott Cain <sc...@sc...> wrote:
>
>
>
>
>
> On Tue, Aug 13, 2019 at 11:00 AM Yang, Chin-Rang (NIH/NHLBI) [E] <
> chi...@ni...> wrote:
>
> Hi Scott,
>
>
>
> Thank you for your prompt reply.
>
>
>
> Yes, my plan is to setup a web server for others to access my data in the
> future.
>
> I was thinking to test it out in a local machine first.
>
>
>
> The error message I found from the Chrome browser is
>
> “Failed to load resource: the server responded with a status
> main.bundle.js:1 of 404 (Not Found)”
>
>
>
> Thank you very much for your advice.
>
> I will talk to our IT people to see how to get an access for a web server
> as well.
>
>
>
>
>
> Chin-Rang
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Tuesday, August 13, 2019 1:46 PM
> *To:* Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] jBrowse set up issue
>
>
>
> Hi Chin-Rang,
>
>
>
> I have a few suggestions: First, if you are only looking to display your
> RNASeq reads locally, you'll probably find it a lot easier to use the
> JBrowse desktop application: https://jbrowse.org/docs/jbrowse_desktop.html
> (download at http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html).
> It's JBrowse running in an Electron wrapper, so you don't have to deal with
> a webserver at all.
>
>
>
> On the other hand if your goal is to get a server running so you can share
> it with lab mates or the like, you can continue down the road using a
> webserver.  I have no experience trying to set up JBrowse on a Windows
> machine.  While the webserver part should work fine, I would guess that
> you're likely to run into problems running the processing perl scripts like
> prepare-refseqs.pl and flatfile-to-json.pl, but that's a step or two away
> at the moment.  To address your immediate problem, please open your
> javascript console to see if there are any errors that might help us figure
> out what's going on.
>
>
>
> Good luck,
>
> Scott
>
>
>
>
>
> On Tue, Aug 13, 2019 at 10:07 AM Yang, Chin-Rang (NIH/NHLBI) [E] via
> Gmod-ajax <gmo...@li...> wrote:
>
> Hi,
>
>
>
> I am trying to setup jBrowse on a Apache server at the local Windows 10
> workstation to display my RNA-Seq data.
>
>
>
> The Apache server is running OK. Test web page shows “It works”.
>
>
>
> I put the Jbrowse folder in the Apache htdocs folder.
>
>
>
> When I run
>
> http://localhost/jbrowse/
>
> the web page shows “ Loading …”
>
>
>
> I tried the “volvox” example, get tracks.conf, volvox.fa, volvox.fa.fai in
> the data folder.
>
> Then run
>
> http://localhost/jbrowse/?data=data
>
> the web page shows “Loading …”, but nothing loaded …
>
>
>
> I am wondering if other people have the similar issue.
>
> Do I need to set jbrowse up in a really working web server, not a local
> one?
>
>
>
> Please advise. Thank you.
>
>
>
> Chin-Rang
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] jBrowse set up issue

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

On Tue, Aug 13, 2019 at 11:00 AM Yang, Chin-Rang (NIH/NHLBI) [E] <
chi...@ni...> wrote:

> Hi Scott,
>
>
>
> Thank you for your prompt reply.
>
>
>
> Yes, my plan is to setup a web server for others to access my data in the
> future.
>
> I was thinking to test it out in a local machine first.
>
>
>
> The error message I found from the Chrome browser is
>
> “Failed to load resource: the server responded with a status
> main.bundle.js:1 of 404 (Not Found)”
>
>
>
> Thank you very much for your advice.
>
> I will talk to our IT people to see how to get an access for a web server
> as well.
>
>
>
>
>
> Chin-Rang
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Tuesday, August 13, 2019 1:46 PM
> *To:* Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] jBrowse set up issue
>
>
>
> Hi Chin-Rang,
>
>
>
> I have a few suggestions: First, if you are only looking to display your
> RNASeq reads locally, you'll probably find it a lot easier to use the
> JBrowse desktop application: https://jbrowse.org/docs/jbrowse_desktop.html
> (download at http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html).
> It's JBrowse running in an Electron wrapper, so you don't have to deal with
> a webserver at all.
>
>
>
> On the other hand if your goal is to get a server running so you can share
> it with lab mates or the like, you can continue down the road using a
> webserver.  I have no experience trying to set up JBrowse on a Windows
> machine.  While the webserver part should work fine, I would guess that
> you're likely to run into problems running the processing perl scripts like
> prepare-refseqs.pl and flatfile-to-json.pl, but that's a step or two away
> at the moment.  To address your immediate problem, please open your
> javascript console to see if there are any errors that might help us figure
> out what's going on.
>
>
>
> Good luck,
>
> Scott
>
>
>
>
>
> On Tue, Aug 13, 2019 at 10:07 AM Yang, Chin-Rang (NIH/NHLBI) [E] via
> Gmod-ajax <gmo...@li...> wrote:
>
> Hi,
>
>
>
> I am trying to setup jBrowse on a Apache server at the local Windows 10
> workstation to display my RNA-Seq data.
>
>
>
> The Apache server is running OK. Test web page shows “It works”.
>
>
>
> I put the Jbrowse folder in the Apache htdocs folder.
>
>
>
> When I run
>
> http://localhost/jbrowse/
>
> the web page shows “ Loading …”
>
>
>
> I tried the “volvox” example, get tracks.conf, volvox.fa, volvox.fa.fai in
> the data folder.
>
> Then run
>
> http://localhost/jbrowse/?data=data
>
> the web page shows “Loading …”, but nothing loaded …
>
>
>
> I am wondering if other people have the similar issue.
>
> Do I need to set jbrowse up in a really working web server, not a local
> one?
>
>
>
> Please advise. Thank you.
>
>
>
> Chin-Rang
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] jBrowse set up issue

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

Hi Chin-Rang,

I have a few suggestions: First, if you are only looking to display your
RNASeq reads locally, you'll probably find it a lot easier to use the
JBrowse desktop application: https://jbrowse.org/docs/jbrowse_desktop.html
(download at http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html).  It's
JBrowse running in an Electron wrapper, so you don't have to deal with a
webserver at all.

On the other hand if your goal is to get a server running so you can share
it with lab mates or the like, you can continue down the road using a
webserver.  I have no experience trying to set up JBrowse on a Windows
machine.  While the webserver part should work fine, I would guess that
you're likely to run into problems running the processing perl scripts like
prepare-refseqs.pl and flatfile-to-json.pl, but that's a step or two away
at the moment.  To address your immediate problem, please open your
javascript console to see if there are any errors that might help us figure
out what's going on.

Good luck,
Scott


On Tue, Aug 13, 2019 at 10:07 AM Yang, Chin-Rang (NIH/NHLBI) [E] via
Gmod-ajax <gmo...@li...> wrote:

> Hi,
>
>
>
> I am trying to setup jBrowse on a Apache server at the local Windows 10
> workstation to display my RNA-Seq data.
>
>
>
> The Apache server is running OK. Test web page shows “It works”.
>
>
>
> I put the Jbrowse folder in the Apache htdocs folder.
>
>
>
> When I run
>
> http://localhost/jbrowse/
>
> the web page shows “ Loading …”
>
>
>
> I tried the “volvox” example, get tracks.conf, volvox.fa, volvox.fa.fai in
> the data folder.
>
> Then run
>
> http://localhost/jbrowse/?data=data
>
> the web page shows “Loading …”, but nothing loaded …
>
>
>
> I am wondering if other people have the similar issue.
>
> Do I need to set jbrowse up in a really working web server, not a local
> one?
>
>
>
> Please advise. Thank you.
>
>
>
> Chin-Rang
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] jBrowse set up issue

[Yang, Chin-R. (NIH/N. [E] <chi...@ni...>]

Hi Scott,

Thank you for your prompt reply.

Yes, my plan is to setup a web server for others to access my data in the future.
I was thinking to test it out in a local machine first.

The error message I found from the Chrome browser is
“Failed to load resource: the server responded with a status main.bundle.js:1 of 404 (Not Found)”

Thank you very much for your advice.
I will talk to our IT people to see how to get an access for a web server as well.


Chin-Rang


From: Scott Cain <sc...@sc...>
Sent: Tuesday, August 13, 2019 1:46 PM
To: Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] jBrowse set up issue

Hi Chin-Rang,

I have a few suggestions: First, if you are only looking to display your RNASeq reads locally, you'll probably find it a lot easier to use the JBrowse desktop application: https://jbrowse.org/docs/jbrowse_desktop.html (download at http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html).  It's JBrowse running in an Electron wrapper, so you don't have to deal with a webserver at all.

On the other hand if your goal is to get a server running so you can share it with lab mates or the like, you can continue down the road using a webserver.  I have no experience trying to set up JBrowse on a Windows machine.  While the webserver part should work fine, I would guess that you're likely to run into problems running the processing perl scripts like prepare-refseqs.pl<http://prepare-refseqs.pl> and flatfile-to-json.pl<http://flatfile-to-json.pl>, but that's a step or two away at the moment.  To address your immediate problem, please open your javascript console to see if there are any errors that might help us figure out what's going on.

Good luck,
Scott


On Tue, Aug 13, 2019 at 10:07 AM Yang, Chin-Rang (NIH/NHLBI) [E] via Gmod-ajax <gmo...@li...<mailto:gmo...@li...>> wrote:
Hi,

I am trying to setup jBrowse on a Apache server at the local Windows 10 workstation to display my RNA-Seq data.

The Apache server is running OK. Test web page shows “It works”.

I put the Jbrowse folder in the Apache htdocs folder.

When I run
http://localhost/jbrowse/
the web page shows “ Loading …”

I tried the “volvox” example, get tracks.conf, volvox.fa, volvox.fa.fai in the data folder.
Then run
http://localhost/jbrowse/?data=data
the web page shows “Loading …”, but nothing loaded …

I am wondering if other people have the similar issue.
Do I need to set jbrowse up in a really working web server, not a local one?

Please advise. Thank you.

Chin-Rang

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


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] jBrowse set up issue

[Yang, Chin-R. (NIH/N. [E] <chi...@ni...>]

Hi,

I am trying to setup jBrowse on a Apache server at the local Windows 10 workstation to display my RNA-Seq data.

The Apache server is running OK. Test web page shows "It works".

I put the Jbrowse folder in the Apache htdocs folder.

When I run
http://localhost/jbrowse/
the web page shows " Loading ..."

I tried the "volvox" example, get tracks.conf, volvox.fa, volvox.fa.fai in the data folder.
Then run
http://localhost/jbrowse/?data=data
the web page shows "Loading ...", but nothing loaded ...

I am wondering if other people have the similar issue.
Do I need to set jbrowse up in a really working web server, not a local one?

Please advise. Thank you.

Chin-Rang

Re: [Gmod-ajax] generate-names.pl does not have any effect

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

Hi there,
The main thing to note is that generate-names.pl does not accept a specific
file as input. By default,  generate-names.pl runs on the whole data data
directory that you provide to the --out parameter, so you just use

bin/generate-names.pl --out /efs/apollo/Nitab-v4.5

This automatically detects the tracks you have loaded in this directory and
populates the "names" folder.

You can use the -v argument to get verbose.

The --tracks argument can accept a list of comma separated track "labels"
from the trackList.json/tracks.conf

-Colin

On Mon, Aug 12, 2019 at 8:39 AM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi Scott,
> I think, I ran *flatfile-to-json.pl <http://flatfile-to-json.pl>* first
> and it generated the following folders:
>
>
>
>
>
>
>
>
>
>
>
> */efs/apollo/Nitab-v4.5$ ls -hlattotal 4.1Gdrwxr-sr-x 10 ubuntu
> apollo_users 6.0K Aug 12 04:16 ..-rw-rw-r--  1 ubuntu apollo_users  541 Aug
> 11 23:33 .htaccessdrwxrwsr-x  2 ubuntu apollo_users  14K Aug 11 23:05
> names-rw-rw-r--  1 ubuntu apollo_users  819 Aug 11 23:04
> trackList.jsondrwxrwsr-x  4 ubuntu apollo_users 6.0K Jul 14 22:23
> tracks-rw-rw-r--  1 ubuntu apollo_users    0 Jul 14 12:21
> tracks.confdrwxrwsr-x 26 ubuntu apollo_users 6.0K Jul 14 12:21
> seq-rw-rw-r--  1 ubuntu apollo_users  49M Jul 14 02:39
> Nitab-v4.5_gene_models_Chr_Edwards2017.gff-rw-rw-r--  1 ubuntu apollo_users
> 2.8G Jul 14 02:24 Nitab-v4.5_genome_Chr_Edwards2017.fasta*
>
> What did I miss?
>
> Thank you in advance,
>
> Michal
>
> On Mon, Aug 12, 2019 at 2:57 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Michal,
>>
>> Did you run flatfile-to-json.pl first? It creates a set of names.txt
>> files that are required for generate-names to work on.
>>
>> Scott
>>
>>
>> On Aug 11, 2019, at 7:20 PM, Michał T. Lorenc <m.t...@gm...>
>> wrote:
>>
>> Hi all,
>> I tried to use `generate-names.pl` in the following way:
>>
>> ```
>>
>> *> /efs/apollo/Nitab-v4.5$ perl
>> ~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl
>> <http://prepare-refseqs.pl> --fasta
>> /efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out
>> /efs/apollo/Nitab-v4.5> /efs/apollo/Nitab-v4.5$ perl
>> ~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl
>> <http://generate-names.pl> --tracks
>> Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5*
>> ```
>> on the below GFF3 file:
>> ```
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *> cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff...Nt01    maker   gene
>>    513567  517023  .       -       .
>> ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367Nt01
>>    maker   mRNA    513567  517023  .       -       .
>> ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal
>> protein S6%2C plastid/chloroplast%2C Translation elongation factor
>> EF1B/ribosomal protein S6%2C Ribosomal protein S6"Nt01    maker   exon
>>  513567  513979  .       -       .
>> ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1Nt01
>>  maker   exon    516618  517023  .       -       .
>> ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1Nt01
>>  maker   five_prime_UTR  516963  517023  .       -       .
>> ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1Nt01
>>    maker   CDS     516618  516962  .       -       0
>> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
>>   CDS     513740  513979  .       -       0
>> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
>>   three_prime_UTR 513567  513739  .       -       .
>> ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1*
>> ```
>>
>> Unfortunately, it did not work. What did I miss?
>>
>> Thank you in advance.
>>
>> Michal
>>
>> _______________________________________________
>> 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] generate-names.pl does not have any effect

[Michał T. L. <m.t...@gm...>]

Hi Scott,
I think, I ran *flatfile-to-json.pl <http://flatfile-to-json.pl>* first and
it generated the following folders:











*/efs/apollo/Nitab-v4.5$ ls -hlattotal 4.1Gdrwxr-sr-x 10 ubuntu
apollo_users 6.0K Aug 12 04:16 ..-rw-rw-r--  1 ubuntu apollo_users  541 Aug
11 23:33 .htaccessdrwxrwsr-x  2 ubuntu apollo_users  14K Aug 11 23:05
names-rw-rw-r--  1 ubuntu apollo_users  819 Aug 11 23:04
trackList.jsondrwxrwsr-x  4 ubuntu apollo_users 6.0K Jul 14 22:23
tracks-rw-rw-r--  1 ubuntu apollo_users    0 Jul 14 12:21
tracks.confdrwxrwsr-x 26 ubuntu apollo_users 6.0K Jul 14 12:21
seq-rw-rw-r--  1 ubuntu apollo_users  49M Jul 14 02:39
Nitab-v4.5_gene_models_Chr_Edwards2017.gff-rw-rw-r--  1 ubuntu apollo_users
2.8G Jul 14 02:24 Nitab-v4.5_genome_Chr_Edwards2017.fasta*

What did I miss?

Thank you in advance,

Michal

On Mon, Aug 12, 2019 at 2:57 PM Scott Cain <sc...@sc...> wrote:

> Hi Michal,
>
> Did you run flatfile-to-json.pl first? It creates a set of names.txt
> files that are required for generate-names to work on.
>
> Scott
>
>
> On Aug 11, 2019, at 7:20 PM, Michał T. Lorenc <m.t...@gm...>
> wrote:
>
> Hi all,
> I tried to use `generate-names.pl` in the following way:
>
> ```
>
> *> /efs/apollo/Nitab-v4.5$ perl
> ~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl
> <http://prepare-refseqs.pl> --fasta
> /efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out
> /efs/apollo/Nitab-v4.5> /efs/apollo/Nitab-v4.5$ perl
> ~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl
> <http://generate-names.pl> --tracks
> Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5*
> ```
> on the below GFF3 file:
> ```
>
>
>
>
>
>
>
>
>
> *> cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff...Nt01    maker   gene
>  513567  517023  .       -       .
> ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367Nt01
>    maker   mRNA    513567  517023  .       -       .
> ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal
> protein S6%2C plastid/chloroplast%2C Translation elongation factor
> EF1B/ribosomal protein S6%2C Ribosomal protein S6"Nt01    maker   exon
>  513567  513979  .       -       .
> ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1Nt01
>  maker   exon    516618  517023  .       -       .
> ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1Nt01
>  maker   five_prime_UTR  516963  517023  .       -       .
> ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1Nt01
>    maker   CDS     516618  516962  .       -       0
> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
>   CDS     513740  513979  .       -       0
> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
>   three_prime_UTR 513567  513739  .       -       .
> ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1*
> ```
>
> Unfortunately, it did not work. What did I miss?
>
> Thank you in advance.
>
> Michal
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] generate-names.pl does not have any effect

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

Hi Michal,

Did you run flatfile-to-json.pl first? It creates a set of names.txt files that are required for generate-names to work on. 

Scott


> On Aug 11, 2019, at 7:20 PM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi all,
> I tried to use `generate-names.pl` in the following way:
> 
> ```
> > /efs/apollo/Nitab-v4.5$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl --fasta /efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out /efs/apollo/Nitab-v4.5
> > /efs/apollo/Nitab-v4.5$ perl ~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl --tracks Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5
> ```
> on the below GFF3 file:
> ```
> > cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff
> ...
> Nt01    maker   gene    513567  517023  .       -       .       ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367
> Nt01    maker   mRNA    513567  517023  .       -       .       ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal protein S6%2C plastid/chloroplast%2C Translation elongation factor EF1B/ribosomal protein S6%2C Ribosomal protein S6"
> Nt01    maker   exon    513567  513979  .       -       .       ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1
> Nt01    maker   exon    516618  517023  .       -       .       ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1
> Nt01    maker   five_prime_UTR  516963  517023  .       -       .       ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1
> Nt01    maker   CDS     516618  516962  .       -       0       ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1
> Nt01    maker   CDS     513740  513979  .       -       0       ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1
> Nt01    maker   three_prime_UTR 513567  513739  .       -       .       ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1
> ```
> 
> Unfortunately, it did not work. What did I miss?
> 
> Thank you in advance.
> 
> Michal
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] generate-names.pl does not have any effect

[Michał T. L. <m.t...@gm...>]

Hi all,
I tried to use `generate-names.pl` in the following way:

```

*> /efs/apollo/Nitab-v4.5$ perl
~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl
<http://prepare-refseqs.pl> --fasta
/efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out
/efs/apollo/Nitab-v4.5> /efs/apollo/Nitab-v4.5$ perl
~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl
<http://generate-names.pl> --tracks
Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5*
```
on the below GFF3 file:
```









*> cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff...Nt01    maker   gene
 513567  517023  .       -       .
ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367Nt01
   maker   mRNA    513567  517023  .       -       .
ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal
protein S6%2C plastid/chloroplast%2C Translation elongation factor
EF1B/ribosomal protein S6%2C Ribosomal protein S6"Nt01    maker   exon
 513567  513979  .       -       .
ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1Nt01
 maker   exon    516618  517023  .       -       .
ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1Nt01
 maker   five_prime_UTR  516963  517023  .       -       .
ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1Nt01
   maker   CDS     516618  516962  .       -       0
ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
  CDS     513740  513979  .       -       0
ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01    maker
  three_prime_UTR 513567  513739  .       -       .
ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1*
```

Unfortunately, it did not work. What did I miss?

Thank you in advance.

Michal

Re: [Gmod-ajax] creating links

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

Hi there,
There are several options for how the action can occur

1. Configuring left-click
2. Configuring right-click menu
3. Customizing the View details popup

These are all documented in the jbrowse docs
https://jbrowse.org/docs/mouse_configs.html

The callback can contain such things like this

function(feature) { return 'http://google.com/?q='+feature.get('Dbxref') }

That will generate a google link for a Dbxref. Note the Dbxref in full is
*TIGRFAM*:TIGR00756 not just the bolded part

It will just take a little javascript if you want to add conditional
statements or parse the string or something like this

-Colin



On Thu, Aug 8, 2019 at 10:50 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi,
> I have below a subset of a GFF3 file which contains different DbXrefs,
> InterProScan accession numbers and GO terms. However, some lines of the
> GFF3 are missing InterProScan accession numbers and GO terms. However, all
> lines contain DbXrefs. Here (https://www.uniprot.org/docs/dbxref) is a
> list of all possible dbxrefs.
>
> How is possible to allow the user to click in JBrowse on a feature and get
> options to be redirected to DbXrefs, InterProScan and ontogy?
>
>    - NbV1Ch09 interpo domain 71124892 71125030 . . . Name=RNase_HI_RT_Ty1;
>    *Dbxref=CDD*:cd09272;Note=CDD
>    - NbV1Ch14 interpo domain 93274595 93274797 . . . Name=Ribonuclease H
>    superfamily;*Dbxref=Gene3D*:G3DSA:3.30.420.10;Note=Gene3D;_Accession=
>    *IPR036397*;Ontology_term=*GO:0003676*
>    - NbV1Ch16 interpo domain 66731787 66732421 . . .
>    Name=Deoxyxylulose-5-phosphate synthase;*Dbxref=Hamap*
>    :MF_00315;Note=Hamap;_Accession=*IPR005477*;Ontology_term=
>    *GO:0008661,GO:0016114*
>    - NbV1Ch09 interpo domain 71124160 71124256 . . . Name=consensus
>    disorder prediction;*Dbxref=MobiDBLite*:mobidb-lite;Note=MobiDBLite
>    - NbV1Ch01 interpo domain 175378467 175379194 . . . Name=AP-1/2/4
>    complex subunit beta;*Dbxref=PIRSF*:PIRSF002291;Note=PIRSF;_Accession=
>    *IPR016342*;Ontology_term=*GO:0015031,GO:0030276*
>    - NbV1Ch07 interpo domain 107909842 107909860 . . . Name=Recoverin
>    family signature;*Dbxref=PRINTS*:PR00450;Note=PRINTS
>    - NbV1Ch09 interpo domain 71123771 71123905 . . . Name=gag-polypeptide
>    of LTR copia-type;*Dbxref=Pfam*:PF14223;Note=Pfam
>    - NbV1Ch03 interpo domain 33983707 33983721 . . . Name=Trp-Asp (WD)
>    repeats signature.;*Dbxref=ProSitePatterns*
>    :PS00678;Note=ProSitePatterns;_Accession=*IPR019775*
>    - NbV1Ch09 interpo domain 71124317 71124413 . . . Name=Integrase,
>    catalytic core;*Dbxref=ProSiteProfiles*
>    :PS50994;Note=ProSiteProfiles;_Accession=*IPR001584*;Ontology_term=
>    *GO:0015074*
>    - NbV1Ch17 interpo domain 30522620 30522886 . . . Name=C1.5: HAD,
>    Beta-PGM, Phosphatase Like;*Dbxref=SFLD*:SFLDG01129;Note=SFLD
>    - NbV1Ch03 interpo domain 33983723 33983761 . . . Name=WD40 repeat;
>    *Dbxref=SMART*:SM00320;Note=SMART;_Accession=*IPR001680*;Ontology_term=
>    *GO:0005515*
>    - NbV1Ch09 interpo domain 71124311 71124414 . . . Name=Ribonuclease
>    H-like superfamily;*Dbxref=SUPERFAMILY*
>    :SSF53098;Note=SUPERFAMILY;_Accession=*IPR012337*
>    - NbV1Ch01 interpo domain 157928056 157928088 . . . Name=PPR:
>    pentatricopeptide repeat domain;*Dbxref=TIGRFAM*
>    :TIGR00756;Note=TIGRFAM;_Accession=*IPR002885*
>
> Thank you in advance,
>
> Michal
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] creating links

[Michał T. L. <m.t...@gm...>]

Hi,
I have below a subset of a GFF3 file which contains different DbXrefs,
InterProScan accession numbers and GO terms. However, some lines of the
GFF3 are missing InterProScan accession numbers and GO terms. However, all
lines contain DbXrefs. Here (https://www.uniprot.org/docs/dbxref) is a list
of all possible dbxrefs.

How is possible to allow the user to click in JBrowse on a feature and get
options to be redirected to DbXrefs, InterProScan and ontogy?

   - NbV1Ch09 interpo domain 71124892 71125030 . . . Name=RNase_HI_RT_Ty1;
   *Dbxref=CDD*:cd09272;Note=CDD
   - NbV1Ch14 interpo domain 93274595 93274797 . . . Name=Ribonuclease H
   superfamily;*Dbxref=Gene3D*:G3DSA:3.30.420.10;Note=Gene3D;_Accession=
   *IPR036397*;Ontology_term=*GO:0003676*
   - NbV1Ch16 interpo domain 66731787 66732421 . . .
   Name=Deoxyxylulose-5-phosphate synthase;*Dbxref=Hamap*
   :MF_00315;Note=Hamap;_Accession=*IPR005477*;Ontology_term=
   *GO:0008661,GO:0016114*
   - NbV1Ch09 interpo domain 71124160 71124256 . . . Name=consensus
   disorder prediction;*Dbxref=MobiDBLite*:mobidb-lite;Note=MobiDBLite
   - NbV1Ch01 interpo domain 175378467 175379194 . . . Name=AP-1/2/4
   complex subunit beta;*Dbxref=PIRSF*:PIRSF002291;Note=PIRSF;_Accession=
   *IPR016342*;Ontology_term=*GO:0015031,GO:0030276*
   - NbV1Ch07 interpo domain 107909842 107909860 . . . Name=Recoverin
   family signature;*Dbxref=PRINTS*:PR00450;Note=PRINTS
   - NbV1Ch09 interpo domain 71123771 71123905 . . . Name=gag-polypeptide
   of LTR copia-type;*Dbxref=Pfam*:PF14223;Note=Pfam
   - NbV1Ch03 interpo domain 33983707 33983721 . . . Name=Trp-Asp (WD)
   repeats signature.;*Dbxref=ProSitePatterns*
   :PS00678;Note=ProSitePatterns;_Accession=*IPR019775*
   - NbV1Ch09 interpo domain 71124317 71124413 . . . Name=Integrase,
   catalytic core;*Dbxref=ProSiteProfiles*
   :PS50994;Note=ProSiteProfiles;_Accession=*IPR001584*;Ontology_term=
   *GO:0015074*
   - NbV1Ch17 interpo domain 30522620 30522886 . . . Name=C1.5: HAD,
   Beta-PGM, Phosphatase Like;*Dbxref=SFLD*:SFLDG01129;Note=SFLD
   - NbV1Ch03 interpo domain 33983723 33983761 . . . Name=WD40 repeat;
   *Dbxref=SMART*:SM00320;Note=SMART;_Accession=*IPR001680*;Ontology_term=
   *GO:0005515*
   - NbV1Ch09 interpo domain 71124311 71124414 . . . Name=Ribonuclease
   H-like superfamily;*Dbxref=SUPERFAMILY*
   :SSF53098;Note=SUPERFAMILY;_Accession=*IPR012337*
   - NbV1Ch01 interpo domain 157928056 157928088 . . . Name=PPR:
   pentatricopeptide repeat domain;*Dbxref=TIGRFAM*
   :TIGR00756;Note=TIGRFAM;_Accession=*IPR002885*

Thank you in advance,

Michal

Re: [Gmod-ajax] Description

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

Hi Michał,

Can you be a little more specific when you say it doesn't work for BED
data?  What doesn't work, hiding the labels or displaying the data at all
or something else?

Thanks,
Scott


On Wed, Aug 7, 2019 at 6:45 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi Scott,
> Thank you it worked for GFF3 files but it does not work for the below BED
> file:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *      {         "category" : "iii. ChIP-seq",         "compress" : 1,
>      "key" : "QldK9.bed",         "label" : "QldK9.bed",
>  "storeClass" : "JBrowse/Store/SeqFeature/NCList",         "style" : {
>       "className" : "feature",            "label" : false         },
>  "trackType" : "CanvasFeatures",         "type" : "CanvasFeatures",
>  "urlTemplate" : "tracks/QldK9.bed/{refseq}/trackData.jsonz"      },*
>
> What did I miss?
>
> Thank you in advance,
>
> Michal
>
>
>
>
> On Wed, Jul 31, 2019 at 3:52 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Michal,
>>
>> Yes, you can suppress the feature labels by adding "label" : false to the
>> style section of the trackList.json config section.
>>
>> For adding a link for a feature, it is moderately more complicated and
>> depends on where you want it to link to.  This section of the docs will get
>> you started:
>>
>>
>> http://jbrowse.org/docs/mouse_configs.html#customizing-left-click-behavior-1
>>
>> but you might need a javascript callback to get it working.  If it's not
>> obvious, please respond and give a description of what you'd like the link
>> to do and we can give you more help.
>>
>> Scott
>>
>>
>> On Tue, Jul 30, 2019 at 10:03 PM Michał T. Lorenc <m.t...@gm...>
>> wrote:
>>
>>> Hi,
>>> I have a GFF3 file with SNPs (please see below) and I loaded it into
>>> Jbrowse/Apollo with *flatfile-to-json.pl <http://flatfile-to-json.pl>
>>> --gff /efs/apollo/snps.fasta.m_snp.gff3 --compress --trackLabel "SNPs"
>>> --out /efs/apollo/ * .
>>>
>>>
>>>
>>> *##gff-version 3NbV1Ch01        SGSautoSNP      SNP     1245    1245
>>>  .       .       .
>>> Name=NbV1ChF00000000000000000001;ID=NbV1ChF00000000000000000001;Contig
>>> name=NbV1Ch01;SNP score=5;SNP pos. on scaffold=1245;Genotype
>>> L=26*T;Genotype Q=5*C;Changes=C/T*
>>> *NbV1Ch01        SGSautoSNP      SNP     1303    1303    .       .
>>> .
>>> Name=NbV1ChF00000000000000000002;ID=NbV1ChF00000000000000000002;Contig
>>> name=NbV1Ch01;SNP score=4;SNP pos. on scaffold=1303;Genotype
>>> L=18*T;Genotype Q=4*A;Changes=A/T*
>>>
>>> [image: image.png]
>>>
>>> How is it possible to hide the SNP description and only show it when the
>>> user mouse over or click on the SNP? Additionally, when the SNP description
>>> appears would it be possible to add a click event to be redirected to a new
>>> page?
>>>
>>> Thank you in advance,
>>>
>>> Best wishes,
>>>
>>> Michal
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Description

[Michał T. L. <m.t...@gm...>]

Hi Scott,
Thank you it worked for GFF3 files but it does not work for the below BED
file:














*      {         "category" : "iii. ChIP-seq",         "compress" : 1,
   "key" : "QldK9.bed",         "label" : "QldK9.bed",         "storeClass"
: "JBrowse/Store/SeqFeature/NCList",         "style" : {
"className" : "feature",            "label" : false         },
 "trackType" : "CanvasFeatures",         "type" : "CanvasFeatures",
 "urlTemplate" : "tracks/QldK9.bed/{refseq}/trackData.jsonz"      },*

What did I miss?

Thank you in advance,

Michal




On Wed, Jul 31, 2019 at 3:52 PM Scott Cain <sc...@sc...> wrote:

> Hi Michal,
>
> Yes, you can suppress the feature labels by adding "label" : false to the
> style section of the trackList.json config section.
>
> For adding a link for a feature, it is moderately more complicated and
> depends on where you want it to link to.  This section of the docs will get
> you started:
>
>
> http://jbrowse.org/docs/mouse_configs.html#customizing-left-click-behavior-1
>
> but you might need a javascript callback to get it working.  If it's not
> obvious, please respond and give a description of what you'd like the link
> to do and we can give you more help.
>
> Scott
>
>
> On Tue, Jul 30, 2019 at 10:03 PM Michał T. Lorenc <m.t...@gm...>
> wrote:
>
>> Hi,
>> I have a GFF3 file with SNPs (please see below) and I loaded it into
>> Jbrowse/Apollo with *flatfile-to-json.pl <http://flatfile-to-json.pl>
>> --gff /efs/apollo/snps.fasta.m_snp.gff3 --compress --trackLabel "SNPs"
>> --out /efs/apollo/ * .
>>
>>
>>
>> *##gff-version 3NbV1Ch01        SGSautoSNP      SNP     1245    1245    .
>>       .       .
>> Name=NbV1ChF00000000000000000001;ID=NbV1ChF00000000000000000001;Contig
>> name=NbV1Ch01;SNP score=5;SNP pos. on scaffold=1245;Genotype
>> L=26*T;Genotype Q=5*C;Changes=C/T*
>> *NbV1Ch01        SGSautoSNP      SNP     1303    1303    .       .
>> .
>> Name=NbV1ChF00000000000000000002;ID=NbV1ChF00000000000000000002;Contig
>> name=NbV1Ch01;SNP score=4;SNP pos. on scaffold=1303;Genotype
>> L=18*T;Genotype Q=4*A;Changes=A/T*
>>
>> [image: image.png]
>>
>> How is it possible to hide the SNP description and only show it when the
>> user mouse over or click on the SNP? Additionally, when the SNP description
>> appears would it be possible to add a click event to be redirected to a new
>> page?
>>
>> Thank you in advance,
>>
>> Best wishes,
>>
>> Michal
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] Description

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

Hi Michal,

Yes, you can suppress the feature labels by adding "label" : false to the
style section of the trackList.json config section.

For adding a link for a feature, it is moderately more complicated and
depends on where you want it to link to.  This section of the docs will get
you started:


http://jbrowse.org/docs/mouse_configs.html#customizing-left-click-behavior-1

but you might need a javascript callback to get it working.  If it's not
obvious, please respond and give a description of what you'd like the link
to do and we can give you more help.

Scott


On Tue, Jul 30, 2019 at 10:03 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi,
> I have a GFF3 file with SNPs (please see below) and I loaded it into
> Jbrowse/Apollo with *flatfile-to-json.pl <http://flatfile-to-json.pl>
> --gff /efs/apollo/snps.fasta.m_snp.gff3 --compress --trackLabel "SNPs"
> --out /efs/apollo/ * .
>
>
>
> *##gff-version 3NbV1Ch01        SGSautoSNP      SNP     1245    1245    .
>       .       .
> Name=NbV1ChF00000000000000000001;ID=NbV1ChF00000000000000000001;Contig
> name=NbV1Ch01;SNP score=5;SNP pos. on scaffold=1245;Genotype
> L=26*T;Genotype Q=5*C;Changes=C/T*
> *NbV1Ch01        SGSautoSNP      SNP     1303    1303    .       .       .
>
> Name=NbV1ChF00000000000000000002;ID=NbV1ChF00000000000000000002;Contig
> name=NbV1Ch01;SNP score=4;SNP pos. on scaffold=1303;Genotype
> L=18*T;Genotype Q=4*A;Changes=A/T*
>
> [image: image.png]
>
> How is it possible to hide the SNP description and only show it when the
> user mouse over or click on the SNP? Additionally, when the SNP description
> appears would it be possible to add a click event to be redirected to a new
> page?
>
> Thank you in advance,
>
> Best wishes,
>
> Michal
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Description

[Michał T. L. <m.t...@gm...>]

Hi,
I have a GFF3 file with SNPs (please see below) and I loaded it into
Jbrowse/Apollo with *flatfile-to-json.pl <http://flatfile-to-json.pl> --gff
/efs/apollo/snps.fasta.m_snp.gff3 --compress --trackLabel "SNPs" --out
/efs/apollo/ * .



*##gff-version 3NbV1Ch01        SGSautoSNP      SNP     1245    1245    .
    .       .
Name=NbV1ChF00000000000000000001;ID=NbV1ChF00000000000000000001;Contig
name=NbV1Ch01;SNP score=5;SNP pos. on scaffold=1245;Genotype
L=26*T;Genotype Q=5*C;Changes=C/T*
*NbV1Ch01        SGSautoSNP      SNP     1303    1303    .       .       .

Name=NbV1ChF00000000000000000002;ID=NbV1ChF00000000000000000002;Contig
name=NbV1Ch01;SNP score=4;SNP pos. on scaffold=1303;Genotype
L=18*T;Genotype Q=4*A;Changes=A/T*

[image: image.png]

How is it possible to hide the SNP description and only show it when the
user mouse over or click on the SNP? Additionally, when the SNP description
appears would it be possible to add a click event to be redirected to a new
page?

Thank you in advance,

Best wishes,

Michal

Re: [Gmod-ajax] Two problems with the installation process

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

Hi there,
The JBrowse desktop installations don't require the setup.sh script to be
run generally

If you are intending to put your JBrowse instance on the web, you should
use the normal JBrowse-1.16.5.zip or JBrowse-1.16.5-dev.zip

Linking BLAST results to jbrowse can be done using different ways, one way
I have done is using sequenceserver and that doesn't require any special
build of jbrowse. It's not super easy to configure but not too bad either
https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse

-Colin



On Mon, Jul 29, 2019 at 1:58 PM 一恆 <114...@qq...> wrote:

> Hello sir
>     My name is Liangye Xu. I'm Zhiqiang Xia's student. I'm working
> in Chinese Academy of Tropical Agricultural Sciences(CATAS). I want to use
> the JBrowser to show our data of cassava. But in the process of
> installation, I encountered a problem that could not be solved. This is my
> setup.log file. Could you tell me how to solve this problem, thank you very
> much.
>     If I link BLAST results to JBrowse. Do I must setup the development
> version of JBrowser?
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Two problems with the installation process

[<114...@qq...>]

Hello sir    My name is Liangye Xu. I'm Zhiqiang Xia's student. I'm working in Chinese Academy of Tropical Agricultural Sciences(CATAS). I want to use the JBrowser to show our data of cassava. But in the process of installation, I encountered a problem that could not be solved. This is my setup.log file. Could you tell me how to solve this problem, thank you very much.
    If I link BLAST results to JBrowse. Do I must setup the development version of JBrowser?

[Gmod-ajax] ElasticSearch plugin with Apollo

[Michał T. L. <m.t...@gm...>]

Hi,
I tried to install ElasticSearch plugin ( 
https://github.com/elsiklab/jbrowse_elasticsearch ) into Apollo. With the 
following steps:


   1. git clone https://github.com/GMOD/Apollo.git
   2. cd Apollo
   3. I added ElasticSearch to `cat 
   docker-files/docker-apollo-config.groovy`
   
















*```jbrowse {    git {        url = 
"https://github.com/GMOD/jbrowse"        branch = "1.16.4-release"    }    
plugins {     ...        ElasticSearch{            git = 
'https://github.com/elsiklab/jbrowse_elasticsearch'            branch = 
'master'            alwaysRecheck = "true"            alwaysPull = 
"true"        }    }}*
``` 
Next, I executed 




*```docker build -t apollo .docker run -it -v "$(pwd)"/mydata:/data -p 
8888:8080 -p 8080:3000 apollo```*

   - http://localhost:8080/ does not work for elasticsearch
   - http://localhost:8888/ only Apollo works without elasticsearch

What did I miss?

Thank you in advance,

Michal

Re: [Gmod-ajax] InterProScan as track

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

Hi Michal, 

The thing that is needed is a tool to map your InterProScan results on to chromosomes. Off hand I don’t know of a generic one but one might exist. I wonder if there is a Galaxy workflow for it. Anyone on the list know?

Scott


> On Jul 25, 2019, at 7:53 AM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi
> I ran InterProScan and I got GFF3, TSV and XML. It appears that the InterProScan's GFF3 file does not contain any chromosome names:
> 
> ```
> ##gff-version 3
> ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
> ##interproscan-version 5.36-75.0
> ##sequence-region g109343.t1 1 1358
> g109343.t1      .       polypeptide     1       1358    .       +       .       ID=g109343.t1;md5=3e908dc966fefe367e64dc9d98b0d3ab
> g109343.t1      ProSiteProfiles protein_match   628     724     18.261  +       .       date=20-07-2019;Target=g109343.t1 628 724;Ontology_term="GO:0015074";ID=match$1_628_724;signature_desc=Integrase c
> atalytic domain profile.;Name=PS50994;status=T;Dbxref="InterPro:IPR001584"
> g109343.t1      SUPERFAMILY     protein_match   586     624     4.19E-5 +       .       date=20-07-2019;Target=g109343.t1 586 624;Ontology_term="GO:0003676","GO:0008270";ID=match$2_586_624;Name=SSF57756
> ;status=T;Dbxref="InterPro:IPR036875"
> g109343.t1      SUPERFAMILY     protein_match   622     725     4.93E-29        +       .       date=20-07-2019;Target=g109343.t1 622 725;ID=match$3_622_725;Name=SSF53098;status=T;Dbxref="InterPro:IPR01
> 2337"
> g109343.t1      ProSiteProfiles protein_match   278     294     9.636   +       .       date=20-07-2019;Target=g109343.t1 278 294;Ontology_term="GO:0003676","GO:0008270";ID=match$4_278_294;signature_des
> c=Zinc finger CCHC-type profile.;Name=PS50158;status=T;Dbxref="InterPro:IPR001878"
> g109343.t1      SMART   protein_match   600     616     0.36    +       .       date=20-07-2019;Target=g109343.t1 600 616;Ontology_term="GO:0003676","GO:0008270";ID=match$5_600_616;Name=SM00343;status=T
> ;Dbxref="InterPro:IPR001878"
> g109343.t1      SMART   protein_match   278     294     6.3E-4  +       .       date=20-07-2019;Target=g109343.t1 278 294;Ontology_term="GO:0003676","GO:0008270";ID=match$5_278_294;Name=SM00343;status=T
> ;Dbxref="InterPro:IPR001878"
> g109343.t1      Pfam    protein_match   82      216     1.2E-24 +       .       date=20-07-2019;Target=g109343.t1 82 216;ID=match$6_82_216;signature_desc=gag-polypeptide of LTR copia-type;Name=PF14223;s
> tatus=T
> ```
> Is there a solution how to load InterProScan results as a track into JBrowse?
> 
> Thank you in advance,
> 
> Michal
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] InterProScan as track

[Michał T. L. <m.t...@gm...>]

Hi
I ran InterProScan and I got GFF3, TSV and XML. It appears that the
InterProScan's GFF3 file does not contain any chromosome names:

```


















*##gff-version 3##feature-ontology
http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
<http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269>##interproscan-version
5.36-75.0##sequence-region g109343.t1 1 1358g109343.t1      .
polypeptide     1       1358    .       +       .
ID=g109343.t1;md5=3e908dc966fefe367e64dc9d98b0d3abg109343.t1
 ProSiteProfiles protein_match   628     724     18.261  +       .
date=20-07-2019;Target=g109343.t1 628
724;Ontology_term="GO:0015074";ID=match$1_628_724;signature_desc=Integrase
catalytic domain
profile.;Name=PS50994;status=T;Dbxref="InterPro:IPR001584"g109343.t1
 SUPERFAMILY     protein_match   586     624     4.19E-5 +       .
date=20-07-2019;Target=g109343.t1 586
624;Ontology_term="GO:0003676","GO:0008270";ID=match$2_586_624;Name=SSF57756;status=T;Dbxref="InterPro:IPR036875"g109343.t1
     SUPERFAMILY     protein_match   622     725     4.93E-29        +
  .       date=20-07-2019;Target=g109343.t1 622
725;ID=match$3_622_725;Name=SSF53098;status=T;Dbxref="InterPro:IPR012337"g109343.t1
     ProSiteProfiles protein_match   278     294     9.636   +       .
  date=20-07-2019;Target=g109343.t1 278
294;Ontology_term="GO:0003676","GO:0008270";ID=match$4_278_294;signature_desc=Zinc
finger CCHC-type
profile.;Name=PS50158;status=T;Dbxref="InterPro:IPR001878"g109343.t1
 SMART   protein_match   600     616     0.36    +       .
date=20-07-2019;Target=g109343.t1 600
616;Ontology_term="GO:0003676","GO:0008270";ID=match$5_600_616;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
     SMART   protein_match   278     294     6.3E-4  +       .
date=20-07-2019;Target=g109343.t1 278
294;Ontology_term="GO:0003676","GO:0008270";ID=match$5_278_294;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
     Pfam    protein_match   82      216     1.2E-24 +       .
date=20-07-2019;Target=g109343.t1 82
216;ID=match$6_82_216;signature_desc=gag-polypeptide of LTR
copia-type;Name=PF14223;status=T*
```
Is there a solution how to load InterProScan results as a track into
JBrowse?

Thank you in advance,

Michal

Re: [Gmod-ajax] problems with RGB coloring of BED file

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

Hello Yael,

I'm not sure the coloring works with BED files imported using
flatfile-to-json, but it should work if you index the BED file and use it
directly. So, for example, if you had a file test.bed in your data/ directory,
you could do `bgzip test.bed` and then `tabix test.bed.gz` (bgzip and tabix
are from htslib <https://www.htslib.org/>). Then add the following lines to
data/tracks.conf:

[tracks.test1]
urlTemplate=test.bed.gz

This should add the new track called "test1" that has the coloring you
want. You can read more about indexed file formats here:
http://jbrowse.org/docs/tutorial.html

Best,
Garrett

On Wed, Jul 24, 2019 at 12:50 PM Yael Altuvia <ya...@gm...> wrote:

>
> Hi,
>
> We are now trying to switch from using the UCSC browser to JBrowse
> (version 2.1) for some specific organisms
> We use firefox browser in a unix environment
>
> We found JBrowse to be very useful for our purpose.
>
> We are now trying to to upload BED file with multiple coloring
>
> example input lines of my BED file
>
> chr     3635789 3635819 NB500937:176:HNWM7AFXX:1:11207:14092:2893_5p    0
>       +       3635789 3635819 255,0,0
> chr     2364664 2364721 NB500937:176:HNWM7AFXX:1:11207:14092:2893_3p    0
>       +       2364664 2364721 51,102,255
> chr     1798195 1798236 NB500937:176:HNWM7AFXX:3:11511:24854:8176_5p    0
>       -       1798195 1798236 255,0,0
> chr     2364637 2364676 NB500937:176:HNWM7AFXX:3:11511:24854:8176_3p    0
>       +       2364637 2364676 51,102,255
> chr     1047431 1047504 NB500937:176:HNWM7AFXX:2:21101:21711:9398_5p    0
>       -       1047431 1047504 255,0,0
> chr     2364637 2364675 NB500937:176:HNWM7AFXX:2:21101:21711:9398_3p    0
>       +       2364637 2364675 51,102,255
> chr     1204394 1204438 NB500937:176:HNWM7AFXX:1:11310:23077:3067_5p    0
>       -       1204394 1204438 255,0,0
> chr     2364664 2364721 NB500937:176:HNWM7AFXX:1:11310:23077:3067_3p    0
>       +       2364664 2364721 51,102,255
>
> We use the following rflatfile-to-json.pl  run command:
>
> /home/www/html/millstone/jbrowse/bin/flatfile-to-json.pl --bed temp.test
> --out <OUT-DIR> --trackType CanvasFeatures --clientConfig '{"showLabels":
> false,"height": 1,"marginBottom": 0.5,"strandArrow": false}' --config
> '{"ItemRgb": true}' --tracklabel temptest1
>
> The generated track is loaded and presented, however all elements are
> colored  golenrod and not according to the BED specifications
>
> We tried  to add "glyph": "BED"
> but then the track is not loaded properly - it is showing "loading" for
> long time even for the smallest file with only 10 lines
>
> These are the attributed seen with the edit option of the track:
> {
>   "maxFeatureSizeForUnderlyingRefSeq": 250000,
>   "maxFeatureScreenDensity": 3,
>   "maxFeatureGlyphExpansion": 500,
>   "maxHeight": 600,
>   "histograms": {
>     "description": "feature density",
>     "min": 0,
>     "height": 100,
>     "color": "goldenrod",
>     "clip_marker_color": "red"
>   },
>   "style": {
>     "_defaultHistScale": 4,
>     "_defaultLabelScale": 30,
>     "_defaultDescriptionScale": 120,
>     "showLabels": false,
>     "showTooltips": true,
>     "className": "feature",
>     "height": 1,
>     "marginBottom": 0.5,
>     "strandArrow": false
>   },
>   "displayMode": "normal",
>   "events": {},
>   "menuTemplate": [
>     {
>       "label": "View details",
>       "title": "{type} {name}",
>       "action": "contentDialog",
>       "iconClass": "dijitIconTask"
>     },
>     {
>       "iconClass": "dijitIconConnector"
>     },
>     {
>       "iconClass": "dijitIconFilter"
>     }
>   ],
>   "type": "JBrowse/View/Track/CanvasFeatures",
>   "storeClass": "JBrowse/Store/SeqFeature/NCList",
>   "label": "temptest1",
>   "urlTemplate": "tracks/temptest1/{refseq}/trackData.json",
>   "key": "temptest1",
>   "trackType": "CanvasFeatures",
>   "ItemRgb": true,
>   "compress": 0,
>   "baseUrl": "
> http://menash.md.huji.ac.il/millstone/jbrowse/data/dir-for-gianluca//",
>   "index": 9,
>   "metadata": {}
> }
>
>
> What are we doing wrong?
>
> Also we would also like to know if it is possible to save a session e.g.
> if tracks were manually edited can they all be saved with the new
> configurations?
>
> Thanks,
> Yael
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] problems with RGB coloring of BED file

[Yael A. <ya...@gm...>]

Hi,

We are now trying to switch from using the UCSC browser to JBrowse (version
2.1) for some specific organisms
We use firefox browser in a unix environment

We found JBrowse to be very useful for our purpose.

We are now trying to to upload BED file with multiple coloring

example input lines of my BED file

chr     3635789 3635819 NB500937:176:HNWM7AFXX:1:11207:14092:2893_5p    0
    +       3635789 3635819 255,0,0
chr     2364664 2364721 NB500937:176:HNWM7AFXX:1:11207:14092:2893_3p    0
    +       2364664 2364721 51,102,255
chr     1798195 1798236 NB500937:176:HNWM7AFXX:3:11511:24854:8176_5p    0
    -       1798195 1798236 255,0,0
chr     2364637 2364676 NB500937:176:HNWM7AFXX:3:11511:24854:8176_3p    0
    +       2364637 2364676 51,102,255
chr     1047431 1047504 NB500937:176:HNWM7AFXX:2:21101:21711:9398_5p    0
    -       1047431 1047504 255,0,0
chr     2364637 2364675 NB500937:176:HNWM7AFXX:2:21101:21711:9398_3p    0
    +       2364637 2364675 51,102,255
chr     1204394 1204438 NB500937:176:HNWM7AFXX:1:11310:23077:3067_5p    0
    -       1204394 1204438 255,0,0
chr     2364664 2364721 NB500937:176:HNWM7AFXX:1:11310:23077:3067_3p    0
    +       2364664 2364721 51,102,255

We use the following rflatfile-to-json.pl  run command:

/home/www/html/millstone/jbrowse/bin/flatfile-to-json.pl --bed temp.test
--out <OUT-DIR> --trackType CanvasFeatures --clientConfig '{"showLabels":
false,"height": 1,"marginBottom": 0.5,"strandArrow": false}' --config
'{"ItemRgb": true}' --tracklabel temptest1

The generated track is loaded and presented, however all elements are
colored  golenrod and not according to the BED specifications

We tried  to add "glyph": "BED"
but then the track is not loaded properly - it is showing "loading" for
long time even for the smallest file with only 10 lines

These are the attributed seen with the edit option of the track:
{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 3,
  "maxFeatureGlyphExpansion": 500,
  "maxHeight": 600,
  "histograms": {
    "description": "feature density",
    "min": 0,
    "height": 100,
    "color": "goldenrod",
    "clip_marker_color": "red"
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": false,
    "showTooltips": true,
    "className": "feature",
    "height": 1,
    "marginBottom": 0.5,
    "strandArrow": false
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconConnector"
    },
    {
      "iconClass": "dijitIconFilter"
    }
  ],
  "type": "JBrowse/View/Track/CanvasFeatures",
  "storeClass": "JBrowse/Store/SeqFeature/NCList",
  "label": "temptest1",
  "urlTemplate": "tracks/temptest1/{refseq}/trackData.json",
  "key": "temptest1",
  "trackType": "CanvasFeatures",
  "ItemRgb": true,
  "compress": 0,
  "baseUrl": "
http://menash.md.huji.ac.il/millstone/jbrowse/data/dir-for-gianluca//",
  "index": 9,
  "metadata": {}
}


What are we doing wrong?

Also we would also like to know if it is possible to save a session e.g. if
tracks were manually edited can they all be saved with the new
configurations?

Thanks,
Yael

Re: [Gmod-ajax] [apollo] InterProScan loading into JBrowse

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

It looks like maybe these annotations are in protein space. I guess what
you are looking for is to convert this protein annotation into genome
coordinates.

This isn't something that is done by jbrowse tools.

I would maybe ask the BRAKER team, as they probably work with this type of
scenario often.

-Colin

On Tue, Jul 23, 2019 at 12:52 PM Lbl <nat...@lb...> wrote:

> Cross posting to jbrowse list
>
> On Jul 23, 2019, at 12:17 AM, Michał T. Lorenc <m.t...@gm...>
> wrote:
>
> Hi
> Our annotation is based on BRAKER2 additionally I ran InterProScan and I
> got GFF3, TSV and XML. I tried to load the GFF3 file using
>
>
> *> perl /apollo/jbrowse/bin/flatfile-to-json.pl
> <http://flatfile-to-json.pl> --gff
> /apollo/braker-soft_utr-interproscan.gff3 --compress --trackType
> HTMLFeatures --trackLabel "interproscan" --out /apollo/*
>
> It appears that no InterProScan results has been loaded. I assume that the
> InterProScan's GFF3 file does not contain any chromosome names:
>
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> *##gff-version 3##feature-ontology
> http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
> <http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269>##interproscan-version
> 5.36-75.0##sequence-region g109343.t1 1 1358g109343.t1      .
> polypeptide     1       1358    .       +       .
> ID=g109343.t1;md5=3e908dc966fefe367e64dc9d98b0d3abg109343.t1
> ProSiteProfiles protein_match   628     724     18.261  +       .
> date=20-07-2019;Target=g109343.t1 628
> 724;Ontology_term="GO:0015074";ID=match$1_628_724;signature_desc=Integrase
> catalytic domain
> profile.;Name=PS50994;status=T;Dbxref="InterPro:IPR001584"g109343.t1
> SUPERFAMILY     protein_match   586     624     4.19E-5 +       .
> date=20-07-2019;Target=g109343.t1 586
> 624;Ontology_term="GO:0003676","GO:0008270";ID=match$2_586_624;Name=SSF57756;status=T;Dbxref="InterPro:IPR036875"g109343.t1
> SUPERFAMILY     protein_match   622     725     4.93E-29        +
> .       date=20-07-2019;Target=g109343.t1 622
> 725;ID=match$3_622_725;Name=SSF53098;status=T;Dbxref="InterPro:IPR012337"g109343.t1
> ProSiteProfiles protein_match   278     294     9.636   +       .
> date=20-07-2019;Target=g109343.t1 278
> 294;Ontology_term="GO:0003676","GO:0008270";ID=match$4_278_294;signature_desc=Zinc
> finger CCHC-type
> profile.;Name=PS50158;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> SMART   protein_match   600     616     0.36    +       .
> date=20-07-2019;Target=g109343.t1 600
> 616;Ontology_term="GO:0003676","GO:0008270";ID=match$5_600_616;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> SMART   protein_match   278     294     6.3E-4  +       .
> date=20-07-2019;Target=g109343.t1 278
> 294;Ontology_term="GO:0003676","GO:0008270";ID=match$5_278_294;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> Pfam    protein_match   82      216     1.2E-24 +       .
> date=20-07-2019;Target=g109343.t1 82
> 216;ID=match$6_82_216;signature_desc=gag-polypeptide of LTR
> copia-type;Name=PF14223;status=T*
>
> Is there a solution how to load InterProScan results as a track into
> JBrowse or are there any scripts which combine InterProScan with BRAKER2?
>
> Thank you in advance,
>
> Michal
>
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