gmod-ajax — JBrowse list

[Gmod-ajax] JBrowse React component

[Adrienne K. <adr...@sf...>]

Hi JBrowse team,


I am using the @jbrowse/react-linear-genome-view component in a React web app. All my input files are GenBank.


My web app currently uses:

- Reference Sequence Track (by converting Genbank to FASTA)

- Feature Track (by converting GenBank to GFF)


What other tracks can I use, if I only have GenBank input files?


I am completely new to bioinformatics and come mainly from a computer science background, so I don't know much about these individual file types and how they work with JBrowse!


I tried creating an Alignments Track (by converting GenBank to BAM), but the `samtools quickcheck` said that the BAM file "had no targets in header", and the JBrowse alignments track said "Error: problem decompressing block: incorrect gzip header check".


Thanks,


Adrienne

Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

Yes you’re right, after seeing the .wiggle file, the refseq IDs don’t match.  I’ll have to get those converted.

Thanks,

Vaneet

From: Scott Cain <sc...@sc...>
Sent: June 26, 2023 1:31 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

[△EXTERNAL]

Hi Vaneet,

Probably the easiest thing to do is to get bigWigToWig from UCSC http://hgdownload.cse.ucsc.edu/admin/exe/ and "decompile" the bigwig so you can open it in a text editor.



On Mon, Jun 26, 2023 at 10:38 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

I understand the issue you’re saying when it comes to gene model and other GFF3 tracks, but how do I see what reference IDs are being used by bigwig tracks?

No I didn’t notice any odd messages in the JS console, thanks for the tip.

Thanks,

Vaneet

From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: June 23, 2023 6:43 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

[△EXTERNAL]

Hi Vaneet,

What are the chances that the names of the reference sequence in the files are like 1,2,3 and in JBrowse they are chr1, chr2, chr3...(or some similar name conflict, like the genbank accession number)? JBrowse 1 isn't brilliant at dealing with these issues (I recall having to hack JB to deal with the fact that sometimes people refer to worm genes like chrI, chrV instead of I, V, etc)

If that's not it, I'm not sure what it might be--are there any messages in the js console?

Scott


On Fri, Jun 23, 2023 at 2:48 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’ve had this issue several times with different batches of RNA-Seq data, related to Echinoderms.  I load a batch of bigwig data tracks and see no visible amplitude or plot anywhere I search in the corresponding genome for any of the tracks.  I attached a screenshot with a few of the tracks and the info box I opened which shows that there should be some score to plot from what I understand, looking at the mean and max values.  Yet I still see nothing plotted.  The person I was working with added the tracks to the IGV browser and it showed that there is data there (screenshot attached), that’s why I’m wondering what’s going on?  Is there some configuration setting I need to enable to show the data which I haven’t thought of?  I can separately send you a link to my JBrowse or send you some of the tracks perhaps for further debugging.

Thanks,

Vaneet

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

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


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

Hi Vaneet,

Probably the easiest thing to do is to get bigWigToWig from UCSC
http://hgdownload.cse.ucsc.edu/admin/exe/ and "decompile" the bigwig so you
can open it in a text editor.



On Mon, Jun 26, 2023 at 10:38 AM Vaneet Lotay <van...@uc...>
wrote:

> Hey Scott,
>
>
>
> I understand the issue you’re saying when it comes to gene model and other
> GFF3 tracks, but how do I see what reference IDs are being used by bigwig
> tracks?
>
>
>
> No I didn’t notice any odd messages in the JS console, thanks for the tip.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* June 23, 2023 6:43 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data
> when there should be
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> What are the chances that the names of the reference sequence in the files
> are like 1,2,3 and in JBrowse they are chr1, chr2, chr3...(or some similar
> name conflict, like the genbank accession number)? JBrowse 1 isn't
> brilliant at dealing with these issues (I recall having to hack JB to deal
> with the fact that sometimes people refer to worm genes like chrI, chrV
> instead of I, V, etc)
>
>
>
> If that's not it, I'm not sure what it might be--are there any messages in
> the js console?
>
>
>
> Scott
>
>
>
>
>
> On Fri, Jun 23, 2023 at 2:48 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’ve had this issue several times with different batches of RNA-Seq data,
> related to Echinoderms.  I load a batch of bigwig data tracks and see no
> visible amplitude or plot anywhere I search in the corresponding genome for
> any of the tracks.  I attached a screenshot with a few of the tracks and
> the info box I opened which shows that there should be some score to plot
> from what I understand, looking at the mean and max values.  Yet I still
> see nothing plotted.  The person I was working with added the tracks to the
> IGV browser and it showed that there is data there (screenshot attached),
> that’s why I’m wondering what’s going on?  Is there some configuration
> setting I need to enable to show the data which I haven’t thought of?  I
> can separately send you a link to my JBrowse or send you some of the tracks
> perhaps for further debugging.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
>
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
>
> WormBase Developer (http://wormbase.org/)
>
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
>
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
>
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

Hey Scott,

I understand the issue you’re saying when it comes to gene model and other GFF3 tracks, but how do I see what reference IDs are being used by bigwig tracks?

No I didn’t notice any odd messages in the JS console, thanks for the tip.

Thanks,

Vaneet

From: Scott Cain <sc...@sc...>
Sent: June 23, 2023 6:43 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

[△EXTERNAL]

Hi Vaneet,

What are the chances that the names of the reference sequence in the files are like 1,2,3 and in JBrowse they are chr1, chr2, chr3...(or some similar name conflict, like the genbank accession number)? JBrowse 1 isn't brilliant at dealing with these issues (I recall having to hack JB to deal with the fact that sometimes people refer to worm genes like chrI, chrV instead of I, V, etc)

If that's not it, I'm not sure what it might be--are there any messages in the js console?

Scott


On Fri, Jun 23, 2023 at 2:48 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’ve had this issue several times with different batches of RNA-Seq data, related to Echinoderms.  I load a batch of bigwig data tracks and see no visible amplitude or plot anywhere I search in the corresponding genome for any of the tracks.  I attached a screenshot with a few of the tracks and the info box I opened which shows that there should be some score to plot from what I understand, looking at the mean and max values.  Yet I still see nothing plotted.  The person I was working with added the tracks to the IGV browser and it showed that there is data there (screenshot attached), that’s why I’m wondering what’s going on?  Is there some configuration setting I need to enable to show the data which I haven’t thought of?  I can separately send you a link to my JBrowse or send you some of the tracks perhaps for further debugging.

Thanks,

Vaneet

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

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


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] modifying display of RNAseq reads

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

Hi there
Great questions

For intron collapsing, some demos and some discussion is here
https://github.com/GMOD/jbrowse-components/issues/557 we do have the
concept of multi region in browse 2 but optimizing it for intron collapse
displays may take some work (e.g. the rna-seq intron arcs may look odd in
the collapsed mode as the beziers would be rendered assuming non-collapsed
genomic coordinates)

For the other questions I can do a bit of investigation. I think color
should be modifiable using the track menu maybe in the latest version
(v2.6.1) but i would have to check. Finally it is not currently possible to
change arc thickness and color. It is good to hear interest in this feature
though, I made an issue here for it. If there are any details on the
coloring scheme you want you can add it here
https://github.com/GMOD/jbrowse-components/issues/3762

-Colin

On Sat, Jun 24, 2023, 2:11 PM Adnan Derti <adn...@gm...> wrote:

> Hi.
>
> I'm using JBrowse2 (desktop v2.5.0) to make plots of RNA-seq data from BAM
> files. I have a few questions about the combination of read counts
> (SNPCoverage) and arcs.
>
> How do I set the color for read counts? They're light gray by default, and
> I can't find a corresponding setting or icon in the settings.
>
> I'd like to reduce the line width and color of arcs, and to make their
> height proportional to counts.
>
> Lastly, it would be great to be able to shrink introns (if you have
> transcripts) to some fixed size, like the multi-region view in the UCSC
> genome browser.
>
> If any of this involves changes to the source code, please feel free to
> point me there.
>
> Thanks!
>
> Adnan
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] modifying display of RNAseq reads

[Adnan D. <adn...@gm...>]

Hi.

I'm using JBrowse2 (desktop v2.5.0) to make plots of RNA-seq data from BAM
files. I have a few questions about the combination of read counts
(SNPCoverage) and arcs.

How do I set the color for read counts? They're light gray by default, and
I can't find a corresponding setting or icon in the settings.

I'd like to reduce the line width and color of arcs, and to make their
height proportional to counts.

Lastly, it would be great to be able to shrink introns (if you have
transcripts) to some fixed size, like the multi-region view in the UCSC
genome browser.

If any of this involves changes to the source code, please feel free to
point me there.

Thanks!

Adnan

Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

Hi Vaneet,

What are the chances that the names of the reference sequence in the files
are like 1,2,3 and in JBrowse they are chr1, chr2, chr3...(or some similar
name conflict, like the genbank accession number)? JBrowse 1 isn't
brilliant at dealing with these issues (I recall having to hack JB to deal
with the fact that sometimes people refer to worm genes like chrI, chrV
instead of I, V, etc)

If that's not it, I'm not sure what it might be--are there any messages in
the js console?

Scott


On Fri, Jun 23, 2023 at 2:48 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I’ve had this issue several times with different batches of RNA-Seq data,
> related to Echinoderms.  I load a batch of bigwig data tracks and see no
> visible amplitude or plot anywhere I search in the corresponding genome for
> any of the tracks.  I attached a screenshot with a few of the tracks and
> the info box I opened which shows that there should be some score to plot
> from what I understand, looking at the mean and max values.  Yet I still
> see nothing plotted.  The person I was working with added the tracks to the
> IGV browser and it showed that there is data there (screenshot attached),
> that’s why I’m wondering what’s going on?  Is there some configuration
> setting I need to enable to show the data which I haven’t thought of?  I
> can separately send you a link to my JBrowse or send you some of the tracks
> perhaps for further debugging.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

one of the most common things that causes this blank track phenomena is the
reference name mismatches e.g. chr1 vs Chr1. happy to check out a link if
you have one though!

On Fri, Jun 23, 2023, 5:48 PM Vaneet Lotay <van...@uc...> wrote:

> Hello,
>
>
>
> I’ve had this issue several times with different batches of RNA-Seq data,
> related to Echinoderms.  I load a batch of bigwig data tracks and see no
> visible amplitude or plot anywhere I search in the corresponding genome for
> any of the tracks.  I attached a screenshot with a few of the tracks and
> the info box I opened which shows that there should be some score to plot
> from what I understand, looking at the mean and max values.  Yet I still
> see nothing plotted.  The person I was working with added the tracks to the
> IGV browser and it showed that there is data there (screenshot attached),
> that’s why I’m wondering what’s going on?  Is there some configuration
> setting I need to enable to show the data which I haven’t thought of?  I
> can separately send you a link to my JBrowse or send you some of the tracks
> perhaps for further debugging.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse bigwig tracks showing no plot/data when there should be

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

Hello,

I've had this issue several times with different batches of RNA-Seq data, related to Echinoderms.  I load a batch of bigwig data tracks and see no visible amplitude or plot anywhere I search in the corresponding genome for any of the tracks.  I attached a screenshot with a few of the tracks and the info box I opened which shows that there should be some score to plot from what I understand, looking at the mean and max values.  Yet I still see nothing plotted.  The person I was working with added the tracks to the IGV browser and it showed that there is data there (screenshot attached), that's why I'm wondering what's going on?  Is there some configuration setting I need to enable to show the data which I haven't thought of?  I can separately send you a link to my JBrowse or send you some of the tracks perhaps for further debugging.

Thanks,

Vaneet

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

Re: [Gmod-ajax] how to use jbrowse2 in a server environment?

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

I think Colin explained the JBrowse2 part very well, I'm just adding some
info about authentication if it will be helpful. We use a LDAP system on
the server end to control access to JBrowse2 instances. The good thing is
it could be used to control access for other services hosted. Like Colin
mentioned, we have multiple instances of JBrowse2 with different
user/access groups.

On Wed, Jun 7, 2023 at 3:35 PM Colin <col...@gm...> wrote:

> Hi Peter
> This is a good question, probably there are many ways to approach this
> depending on your wants/needs
>
> JBrowse 2 itself is sort of 'lightweight' on server resources because it
> doesn't actually run code server side. JBrowse 2 is just
> javascript/css/html that is run on a users client side browser. That means,
> you can create "multiple jbrowse 2 instances" on your server and you don't
> have to worry about any conflicts
>
> For example
>
> cd /var/www/html/
> jbrowse create instance1
> jbrowse create instance2
> jbrowse add-assembly organism1.fa --out instance1 --load copy
> jbrowse add-assembly organism1.fa --out instance2 --load copy
>
> That will create /var/www/html/instance1 and /var/www/html/instance2, that
> can be visited via http://yourhost/instance1 and http://yourhost/instance2,
> each separate jbrowse 2 instances. You could add .htaccess to the instance1
> folder and instance2 folder for different access levels, that would add
> 'simple http authentication'. Little old school, but works :)
>
>
> At one point I wanted to create a demo of this but just wasn't sure how
> best to distribute it (e.g. could create a docker image or just a simple
> FAQ entry documenting the above steps)
>
>
> Also note: we have some interesting workflows inside jbrowse 2 that help
> access authenticated resources from third party websites. This is
> *generally* used when accessing a third party domain e.g. your jbrowse is
> on http://yoursite.com/jbrowse2 but you want to access resources on
> http://someothersite.com/resource. In this case, jbrowse 2 has
> functionality called "internet accounts" that can access those third party
> resources via a number of built in ways, or can be extended to do custom
> stuff if you write plugins. This is likely not something you would need to
> implement if you are in control of your distribution, but could be an
> option. This workflow could also allow there to be a single jbrowse2 folder
> and then you have multiple config files in that folder that have different
> access levels, but this may be more complicated than the above
>
> Also also note: if you are using some sort of framework, and it accepts
> e.g. react components on certain authenticated routes, you can consider
> using our embedded components like @jbrowse/react-linear-genome-view. That
> may be a little more "modern" by some interpretations. We are soon
> releasing the entire "jbrowse web app" as a react component that can be
> installed via NPM (currently only e.g. the linear genome view is on NPM,
> but the full "jbrowse web app" react component will be on NPM pretty soon)
>
> -Colin
>
> On Wed, Jun 7, 2023 at 11:35 AM Peter Minogue via Gmod-ajax <
> gmo...@li...> wrote:
>
>> To the JBrowse 2 team,
>>
>>
>>
>> I was looking at this next-generation genome browser in a Linux server
>> environment. The idea is , have it installed ‘centrally’ on a Linux server
>> and then display it via a browser or so on one’s local machine. This would
>> avoid having to set this up for multiple people. This would require some
>> sort of user authentication I presume on the web application, but I can’t
>> see any mention of it in the documentation. I presume it would just use the
>> Linux authentication subsystem to do this? How does one do this?
>>
>>
>>
>> Considering more people will be doing complete genomes at RSB this kind
>> of setup will become more popular. It is the easiest way to share the
>> assembly and annotation + else within a group using all the users and group
>> file permissions on the central Linux server.
>>
>>
>>
>> Is this possible? Any documentation on doing this? Or is it single
>> user/workstation only application?
>>
>>
>>
>>
>>
>> Cheers
>>
>> Peter
>>
>>
>>
>> ---------------------------------------------------------------
>>
>> Peter Minogue
>>
>> IT Infrastructure
>>
>> Information Technology Services
>>
>> Research School of Biology
>>
>> ANU College of Science, Robertson Bld 46
>>
>> The Australian National University
>>
>> Canberra ACT 2600
>>
>>
>>
>> RSB Service Desk: hel...@an...
>>
>> M 0423 136 495
>>
>> http://biology.anu.edu.au/people/peter-minogue
>>
>> The RSB IT Infrastructure User Documentation is here
>> <https://infrawiki.rsb.anu.edu.au/doku.php?id=rsb_it:infrastructure:userdoco:start>
>>
>> *the Queen said “other capital cities may claim to be centres of
>> transport *
>>
>> *or commerce or military strongholds, but let Canberra's pride be
>> scholarship.”*
>>
>>
>> _______________________________________________
>> 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] how to use jbrowse2 in a server environment?

[Peter M. <pet...@an...>]

Hi Colin,
Thanks for that information. So one could imbed your javascript app inside another that handles user authentication and access control to the filesystem  on the server that the webserver is running on? Perhaps like JupyterLab which spawns a user process to control access rights on the server?


From: Colin <col...@gm...>
Sent: Thursday, 8 June 2023 6:35 AM
To: Peter Minogue <pet...@an...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] how to use jbrowse2 in a server environment?

You don't often get email from col...@gm...<mailto:col...@gm...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Hi Peter
This is a good question, probably there are many ways to approach this depending on your wants/needs

JBrowse 2 itself is sort of 'lightweight' on server resources because it doesn't actually run code server side. JBrowse 2 is just javascript/css/html that is run on a users client side browser. That means, you can create "multiple jbrowse 2 instances" on your server and you don't have to worry about any conflicts

For example

cd /var/www/html/
jbrowse create instance1
jbrowse create instance2
jbrowse add-assembly organism1.fa --out instance1 --load copy
jbrowse add-assembly organism1.fa --out instance2 --load copy

That will create /var/www/html/instance1 and /var/www/html/instance2, that can be visited via http://yourhost/instance1 and http://yourhost/instance2, each separate jbrowse 2 instances. You could add .htaccess to the instance1 folder and instance2 folder for different access levels, that would add 'simple http authentication'. Little old school, but works :)


At one point I wanted to create a demo of this but just wasn't sure how best to distribute it (e.g. could create a docker image or just a simple FAQ entry documenting the above steps)


Also note: we have some interesting workflows inside jbrowse 2 that help access authenticated resources from third party websites. This is *generally* used when accessing a third party domain e.g. your jbrowse is on http://yoursite.com/jbrowse2 but you want to access resources on http://someothersite.com/resource. In this case, jbrowse 2 has functionality called "internet accounts" that can access those third party resources via a number of built in ways, or can be extended to do custom stuff if you write plugins. This is likely not something you would need to implement if you are in control of your distribution, but could be an option. This workflow could also allow there to be a single jbrowse2 folder and then you have multiple config files in that folder that have different access levels, but this may be more complicated than the above

Also also note: if you are using some sort of framework, and it accepts e.g. react components on certain authenticated routes, you can consider using our embedded components like @jbrowse/react-linear-genome-view. That may be a little more "modern" by some interpretations. We are soon releasing the entire "jbrowse web app" as a react component that can be installed via NPM (currently only e.g. the linear genome view is on NPM, but the full "jbrowse web app" react component will be on NPM pretty soon)

-Colin

On Wed, Jun 7, 2023 at 11:35 AM Peter Minogue via Gmod-ajax <gmo...@li...<mailto:gmo...@li...>> wrote:
To the JBrowse 2 team,

I was looking at this next-generation genome browser in a Linux server environment. The idea is , have it installed ‘centrally’ on a Linux server and then display it via a browser or so on one’s local machine. This would avoid having to set this up for multiple people. This would require some sort of user authentication I presume on the web application, but I can’t see any mention of it in the documentation. I presume it would just use the Linux authentication subsystem to do this? How does one do this?

Considering more people will be doing complete genomes at RSB this kind of setup will become more popular. It is the easiest way to share the assembly and annotation + else within a group using all the users and group file permissions on the central Linux server.

Is this possible? Any documentation on doing this? Or is it single user/workstation only application?


Cheers
Peter

---------------------------------------------------------------
Peter Minogue
IT Infrastructure
Information Technology Services
Research School of Biology
ANU College of Science, Robertson Bld 46
The Australian National University
Canberra ACT 2600

RSB Service Desk: hel...@an...<mailto:hel...@an...>
M 0423 136 495
http://biology.anu.edu.au/people/peter-minogue
The RSB IT Infrastructure User Documentation is here<https://infrawiki.rsb.anu.edu.au/doku.php?id=rsb_it:infrastructure:userdoco:start>
the Queen said “other capital cities may claim to be centres of transport
or commerce or military strongholds, but let Canberra's pride be scholarship.”

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

Re: [Gmod-ajax] how to use jbrowse2 in a server environment?

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

Hi Peter
This is a good question, probably there are many ways to approach this
depending on your wants/needs

JBrowse 2 itself is sort of 'lightweight' on server resources because it
doesn't actually run code server side. JBrowse 2 is just
javascript/css/html that is run on a users client side browser. That means,
you can create "multiple jbrowse 2 instances" on your server and you don't
have to worry about any conflicts

For example

cd /var/www/html/
jbrowse create instance1
jbrowse create instance2
jbrowse add-assembly organism1.fa --out instance1 --load copy
jbrowse add-assembly organism1.fa --out instance2 --load copy

That will create /var/www/html/instance1 and /var/www/html/instance2, that
can be visited via http://yourhost/instance1 and http://yourhost/instance2,
each separate jbrowse 2 instances. You could add .htaccess to the instance1
folder and instance2 folder for different access levels, that would add
'simple http authentication'. Little old school, but works :)


At one point I wanted to create a demo of this but just wasn't sure how
best to distribute it (e.g. could create a docker image or just a simple
FAQ entry documenting the above steps)


Also note: we have some interesting workflows inside jbrowse 2 that help
access authenticated resources from third party websites. This is
*generally* used when accessing a third party domain e.g. your jbrowse is
on http://yoursite.com/jbrowse2 but you want to access resources on
http://someothersite.com/resource. In this case, jbrowse 2 has
functionality called "internet accounts" that can access those third party
resources via a number of built in ways, or can be extended to do custom
stuff if you write plugins. This is likely not something you would need to
implement if you are in control of your distribution, but could be an
option. This workflow could also allow there to be a single jbrowse2 folder
and then you have multiple config files in that folder that have different
access levels, but this may be more complicated than the above

Also also note: if you are using some sort of framework, and it accepts
e.g. react components on certain authenticated routes, you can consider
using our embedded components like @jbrowse/react-linear-genome-view. That
may be a little more "modern" by some interpretations. We are soon
releasing the entire "jbrowse web app" as a react component that can be
installed via NPM (currently only e.g. the linear genome view is on NPM,
but the full "jbrowse web app" react component will be on NPM pretty soon)

-Colin

On Wed, Jun 7, 2023 at 11:35 AM Peter Minogue via Gmod-ajax <
gmo...@li...> wrote:

> To the JBrowse 2 team,
>
>
>
> I was looking at this next-generation genome browser in a Linux server
> environment. The idea is , have it installed ‘centrally’ on a Linux server
> and then display it via a browser or so on one’s local machine. This would
> avoid having to set this up for multiple people. This would require some
> sort of user authentication I presume on the web application, but I can’t
> see any mention of it in the documentation. I presume it would just use the
> Linux authentication subsystem to do this? How does one do this?
>
>
>
> Considering more people will be doing complete genomes at RSB this kind of
> setup will become more popular. It is the easiest way to share the assembly
> and annotation + else within a group using all the users and group file
> permissions on the central Linux server.
>
>
>
> Is this possible? Any documentation on doing this? Or is it single
> user/workstation only application?
>
>
>
>
>
> Cheers
>
> Peter
>
>
>
> ---------------------------------------------------------------
>
> Peter Minogue
>
> IT Infrastructure
>
> Information Technology Services
>
> Research School of Biology
>
> ANU College of Science, Robertson Bld 46
>
> The Australian National University
>
> Canberra ACT 2600
>
>
>
> RSB Service Desk: hel...@an...
>
> M 0423 136 495
>
> http://biology.anu.edu.au/people/peter-minogue
>
> The RSB IT Infrastructure User Documentation is here
> <https://infrawiki.rsb.anu.edu.au/doku.php?id=rsb_it:infrastructure:userdoco:start>
>
> *the Queen said “other capital cities may claim to be centres of transport
> *
>
> *or commerce or military strongholds, but let Canberra's pride be
> scholarship.”*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] how to use jbrowse2 in a server environment?

[Peter M. <pet...@an...>]

To the JBrowse 2 team,

I was looking at this next-generation genome browser in a Linux server environment. The idea is , have it installed 'centrally' on a Linux server and then display it via a browser or so on one's local machine. This would avoid having to set this up for multiple people. This would require some sort of user authentication I presume on the web application, but I can't see any mention of it in the documentation. I presume it would just use the Linux authentication subsystem to do this? How does one do this?

Considering more people will be doing complete genomes at RSB this kind of setup will become more popular. It is the easiest way to share the assembly and annotation + else within a group using all the users and group file permissions on the central Linux server.

Is this possible? Any documentation on doing this? Or is it single user/workstation only application?


Cheers
Peter

---------------------------------------------------------------
Peter Minogue
IT Infrastructure
Information Technology Services
Research School of Biology
ANU College of Science, Robertson Bld 46
The Australian National University
Canberra ACT 2600

RSB Service Desk: hel...@an...<mailto:hel...@an...>
M 0423 136 495
http://biology.anu.edu.au/people/peter-minogue
The RSB IT Infrastructure User Documentation is here<https://infrawiki.rsb.anu.edu.au/doku.php?id=rsb_it:infrastructure:userdoco:start>
the Queen said "other capital cities may claim to be centres of transport
or commerce or military strongholds, but let Canberra's pride be scholarship."

Re: [Gmod-ajax] JBrowse2 multi-quantitative tracks

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

Thanks! This is really really helpful! Especially the part that takes the
config JSON block from the UI. This is a great trick!

Thanks!

Ke

On Fri, Jun 2, 2023 at 5:50 PM Colin <col...@gm...> wrote:

> Hi there,
> It's great to hear that MultiBigWig is working for you!
>
> It can be tricky to get some of the precise configs, but one way is to go
> into the configuration editor specifically and then tweak the settings. The
> below config shows that you can set defaultRendering on the "display" to
> enable this.
>
> I also attached to this email some screenshots showing the procedure I use
> to get the right config options
>
> { "type": "MultiQuantitativeTrack", "trackId": "mytrack", "name":
> "MultiBigWig track", "assemblyNames": ["volvox"], "adapter": { "type":
> "MultiWiggleAdapter", "subadapters": [ { "name": "row1", "type":
> "BigWigAdapter", "bigWigLocation": { "uri": "v1.bw" } }, { "name":
> "row2", "type": "BigWigAdapter", "bigWigLocation": {"uri": "v2.bw" } } ]
> }, "displays": [ { "type": "MultiLinearWiggleDisplay", "displayId":
> "mydisplayid-randomnumber-41543514", "defaultRendering": "multirowdensity"
> } ] }
>
>
>
>
> -Colin
>
> On Fri, Jun 2, 2023 at 1:30 PM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I've been using this track type very extensively and it looks great! One
>> small question: in the configuration, is there a way to set the default
>> render type to multirowdensity (for certain data types, density is
>> preferred over xyplot)? I guess it might be a tag/value pair in the JSON
>> block but it seems I can't find the exact syntax for this.
>>
>> Thanks!
>>
>> Ke
>>
> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse2 multi-quantitative tracks

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

Hi there,
It's great to hear that MultiBigWig is working for you!

It can be tricky to get some of the precise configs, but one way is to go
into the configuration editor specifically and then tweak the settings. The
below config shows that you can set defaultRendering on the "display" to
enable this.

I also attached to this email some screenshots showing the procedure I use
to get the right config options

{ "type": "MultiQuantitativeTrack", "trackId": "mytrack", "name":
"MultiBigWig track", "assemblyNames": ["volvox"], "adapter": { "type":
"MultiWiggleAdapter", "subadapters": [ { "name": "row1", "type":
"BigWigAdapter", "bigWigLocation": { "uri": "v1.bw" } }, { "name": "row2",
"type": "BigWigAdapter", "bigWigLocation": {"uri": "v2.bw" } } ] },
"displays": [ { "type": "MultiLinearWiggleDisplay", "displayId":
"mydisplayid-randomnumber-41543514", "defaultRendering": "multirowdensity"
} ] }




-Colin

On Fri, Jun 2, 2023 at 1:30 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I've been using this track type very extensively and it looks great! One
> small question: in the configuration, is there a way to set the default
> render type to multirowdensity (for certain data types, density is
> preferred over xyplot)? I guess it might be a tag/value pair in the JSON
> block but it seems I can't find the exact syntax for this.
>
> Thanks!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 multi-quantitative tracks

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

Hi,

I've been using this track type very extensively and it looks great! One
small question: in the configuration, is there a way to set the default
render type to multirowdensity (for certain data types, density is
preferred over xyplot)? I guess it might be a tag/value pair in the JSON
block but it seems I can't find the exact syntax for this.

Thanks!

Ke

Re: [Gmod-ajax] Problems installing GWAS viewer plugin

[Hans Vasquez-G. <hva...@un...>]

Hi Colin,

Thank you. The header line was the problem.

All the best,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Thursday, May 25, 2023 2:07 PM
To: Hans Vasquez-Gross <hva...@un...>; gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

I think I found the problem
The header line for your BEDTabix file should start with a "#"

Then JBrowse will detect that it is naming the headers and is not a data line
E.g. First line starts with #

#chromosome     base_pair_location      p_value neg_log
10      82228   0.430992        0.365531
10      82636   0.333756        0.476571
10      85696   0.838472        0.0765114
10      86828   0.42009 0.376658
10      88007   0.924451        0.0341161
10      88058   0.924451        0.0341161
10      89716   0.363215        0.439836

I think it'll work after that. Possibly there is a separate bug with the infinite loading instead of reporting blank or error state in v2.1.4 that you are using that may be fixed on latest (v2.5.0 at time of writing) but i think after you adjust the data header, it'll fix it for your version

-Colin


On Thu, May 25, 2023 at 11:46 AM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Correct, I checked the webdeveloper view and aw the following error which seems related to the full plugin. However, the first track is working, soI'm not sure how to proceed with troubleshooting.

Error: NetworkError when attempting to fetch resource. Resource URL: https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js Source Map URL: jbrowse-plugin-gwas.umd.production.min.js.map

Config.json
    {
  "type": "FeatureTrack",
  "trackId": "gwas_track",

  "name": "GWAS example data",
  "category": ["Annotation"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "scoreColumn": "neg_log_pvalue",
    "bedGzLocation": {
      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz"
    },
    "index": {
      "location": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "gwas_display1",
      "type": "LinearManhattanDisplay"
    }
  ]
},
{
  "type": "FeatureTrack",
  "trackId": "gwas_track_parkinsons",
  "name": "GWAS Parkinsons",
  "category": ["Annotation"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "scoreColumn": "neg_log",
    "bedGzLocation": {
      "uri": "GCST011038_buildGRCh37.4col.tsv.gz"
    },
    "index": {
      "location": {
        "uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "gwas_display2",
      "type": "LinearManhattanDisplay"
    }
  ]
}

________________________________
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Thursday, May 25, 2023 10:43 AM
To: Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

What is the issue you are seeing? The second track not loading?

-Colin

On Thu, May 25, 2023 at 11:30 AM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hi Colin,

Just in case you need it for troubleshooting, here is the direct link for this project

https://biox.unr.edu/jbrowse2/?session=share-ODrBC6jY9Q&password=AFRLj

hg19 with the example GWAS data and a sample dataset I downloaded from GWAS Atlas.

Best,
-Hans

________________________________
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Wednesday, May 24, 2023 3:27 PM
To: Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>>
Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>>; Jeremiah B Reyes <jr...@un...<mailto:jr...@un...>>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

Hi there, the error is saying there are two tracks with the same displayId essentially, but the displayId needs to be unique, so you can change the track config to say gwas_viewer1 and gwas_viewer2 (or any random set of unique strings)

Hope that helps!
-Colin

On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I believe I successfully configured the addition of the GWAS plugin within the config.json file.  However, when I try to load the track with the example data, I get the following error:


Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0

How would I go about troubleshooting this error? Any advice would be greatly appreciated.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

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

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un...<mailto:ab...@un...>.

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un...<mailto:ab...@un...>.

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un....

Re: [Gmod-ajax] Problems installing GWAS viewer plugin

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

I think I found the problem
The header line for your BEDTabix file should start with a "#"

Then JBrowse will detect that it is naming the headers and is not a data
line
E.g. First line starts with #

#chromosome     base_pair_location      p_value neg_log
10      82228   0.430992        0.365531
10      82636   0.333756        0.476571
10      85696   0.838472        0.0765114
10      86828   0.42009 0.376658
10      88007   0.924451        0.0341161
10      88058   0.924451        0.0341161
10      89716   0.363215        0.439836

I think it'll work after that. Possibly there is a separate bug with the
infinite loading instead of reporting blank or error state in v2.1.4 that
you are using that may be fixed on latest (v2.5.0 at time of writing) but i
think after you adjust the data header, it'll fix it for your version

-Colin


On Thu, May 25, 2023 at 11:46 AM Hans Vasquez-Gross <hva...@un...>
wrote:

> Correct, I checked the webdeveloper view and aw the following error which
> seems related to the full plugin. However, the first track is working,
> soI'm not sure how to proceed with troubleshooting.
>
> Error: NetworkError when attempting to fetch resource. Resource URL:
> https://unpkg.com/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js
> Source Map URL: jbrowse-plugin-gwas.umd.production.min.js.map
>
> Config.json
>     {
>   "type": "FeatureTrack",
>   "trackId": "gwas_track",
>
>   "name": "GWAS example data",
>   "category": ["Annotation"],
>   "assemblyNames": ["hg19"],
>   "adapter": {
>     "type": "BedTabixAdapter",
>     "scoreColumn": "neg_log_pvalue",
>     "bedGzLocation": {
>       "uri": "
> https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz
> "
>     },
>     "index": {
>       "location": {
>         "uri": "
> https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gwas/summary_stats.txt.gz.tbi
> "
>       },
>       "indexType": "TBI"
>     }
>   },
>   "displays": [
>     {
>       "displayId": "gwas_display1",
>       "type": "LinearManhattanDisplay"
>     }
>   ]
> },
> {
>   "type": "FeatureTrack",
>   "trackId": "gwas_track_parkinsons",
>   "name": "GWAS Parkinsons",
>   "category": ["Annotation"],
>   "assemblyNames": ["hg19"],
>   "adapter": {
>     "type": "BedTabixAdapter",
>     "scoreColumn": "neg_log",
>     "bedGzLocation": {
>       "uri": "GCST011038_buildGRCh37.4col.tsv.gz"
>     },
>     "index": {
>       "location": {
>         "uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
>       },
>       "indexType": "TBI"
>     }
>   },
>   "displays": [
>     {
>       "displayId": "gwas_display2",
>       "type": "LinearManhattanDisplay"
>     }
>   ]
> }
>
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Thursday, May 25, 2023 10:43 AM
> *To:* Hans Vasquez-Gross <hva...@un...>
> *Subject:* Re: [Gmod-ajax] Problems installing GWAS viewer plugin
>
>
> *[EXTERNAL EMAIL]*
>
> What is the issue you are seeing? The second track not loading?
>
> -Colin
>
> On Thu, May 25, 2023 at 11:30 AM Hans Vasquez-Gross <hva...@un...>
> wrote:
>
> Hi Colin,
>
> Just in case you need it for troubleshooting, here is the direct link for
> this project
>
> https://biox.unr.edu/jbrowse2/?session=share-ODrBC6jY9Q&password=AFRLj
>
> hg19 with the example GWAS data and a sample dataset I downloaded from
> GWAS Atlas.
>
> Best,
> -Hans
>
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Wednesday, May 24, 2023 3:27 PM
> *To:* Hans Vasquez-Gross <hva...@un...>
> *Cc:* gmod-ajax <gmo...@li...>; Jeremiah B Reyes <
> jr...@un...>
> *Subject:* Re: [Gmod-ajax] Problems installing GWAS viewer plugin
>
>
> *[EXTERNAL EMAIL]*
>
> Hi there, the error is saying there are two tracks with the same displayId
> essentially, but the displayId needs to be unique, so you can change the
> track config to say gwas_viewer1 and gwas_viewer2 (or any random set of
> unique strings)
>
> Hope that helps!
> -Colin
>
> On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...>
> wrote:
>
> Hello All,
>
> I believe I successfully configured the addition of the GWAS plugin within
> the config.json file.  However, when I try to load the track with the
> example data, I get the following error:
>
> Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0
>
> How would I go about troubleshooting this error? Any advice would be
> greatly appreciated.
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> This email originated outside of the University of Nevada, Reno. Do not
> click on links or attachments unless you recognize the sender and know the
> content is safe. Report suspicious emails to the Office of Information
> Technology (OIT) at ab...@un....
>
>
> This email originated outside of the University of Nevada, Reno. Do not
> click on links or attachments unless you recognize the sender and know the
> content is safe. Report suspicious emails to the Office of Information
> Technology (OIT) at ab...@un....
>
>

Re: [Gmod-ajax] Problems installing GWAS viewer plugin

[Hans Vasquez-G. <hva...@un...>]

I fixed the bug with the neg_log column calculation.  Corrected excerpt below.

gross@salzberg:/var/www/html/jbrowse2$ zcat GCST011038_buildGRCh37.4col.tsv.gz | head
chromosome  base_pair_location      p_value     neg_log
10    82228 0.430992    0.365531
10    82636 0.333756    0.476571
10    85696 0.838472    0.0765114
10    86828 0.42009     0.376658
10    88007 0.924451    0.0341161
10    88058 0.924451    0.0341161
10    89716 0.363215    0.439836
10    89913 0.925755    0.0335039
10    91246 0.873263    0.0588549

________________________________
From: Hans Vasquez-Gross <hva...@un...>
Sent: Wednesday, May 24, 2023 4:17 PM
To: Colin <col...@gm...>
Cc: gmod-ajax <gmo...@li...>; Jeremiah B Reyes <jr...@un...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin

Hi Colin,

Thank you for the feedback. I updated the displayId for the two tracks to be unique.  Now the example data one is working. However, our test file isn't working.

Here is an excerpt from the file. I need to update the calculations for neg_log column because it isn't correct, but I think it should be still enough information to test the GWAS plugin with our own files.
chromosome  base_pair_location      p_value     neg_log
10    82228 0.430992    2.69769
10    82636 0.333756    2.15653
10    85696 0.838472    6.89401
10    86828 0.42009     2.63081
10    88007 0.924451    8.40332
10    88058 0.924451    8.40332
10    89716 0.363215    2.30789
10    89913 0.925755    8.42859
10    91246 0.873263    7.46901


With the config.json excerpt here:
{
  "type": "FeatureTrack",
  "trackId": "gwas_track_parkinsons",
  "name": "GWAS Parkinsons",
  "category": ["Annotation"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "scoreColumn": "neg_log",
    "bedGzLocation": {
      "uri": "GCST011038_buildGRCh37.4col.tsv.gz"
    },
    "index": {
      "location": {
        "uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "gwas_display2",
      "type": "LinearManhattanDisplay"
    }
  ]
}


I created the index with the following command:
tabix -0 -b 2 -s 1 -S 1 -e 2 -f GCST011038_buildGRCh37.4col.tsv.gz

If you need the URL for this jbrowse2 installation for testing, I could provide it to you directly.

Thank you for the advice.

All the best,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, May 24, 2023 3:27 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmod-ajax <gmo...@li...>; Jeremiah B Reyes <jr...@un...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

Hi there, the error is saying there are two tracks with the same displayId essentially, but the displayId needs to be unique, so you can change the track config to say gwas_viewer1 and gwas_viewer2 (or any random set of unique strings)

Hope that helps!
-Colin

On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I believe I successfully configured the addition of the GWAS plugin within the config.json file.  However, when I try to load the track with the example data, I get the following error:


Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0

How would I go about troubleshooting this error? Any advice would be greatly appreciated.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

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

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un....

Re: [Gmod-ajax] Problems installing GWAS viewer plugin

[Hans Vasquez-G. <hva...@un...>]

Hi Colin,

Thank you for the feedback. I updated the displayId for the two tracks to be unique.  Now the example data one is working. However, our test file isn't working.

Here is an excerpt from the file. I need to update the calculations for neg_log column because it isn't correct, but I think it should be still enough information to test the GWAS plugin with our own files.
chromosome  base_pair_location      p_value     neg_log
10    82228 0.430992    2.69769
10    82636 0.333756    2.15653
10    85696 0.838472    6.89401
10    86828 0.42009     2.63081
10    88007 0.924451    8.40332
10    88058 0.924451    8.40332
10    89716 0.363215    2.30789
10    89913 0.925755    8.42859
10    91246 0.873263    7.46901


With the config.json excerpt here:
{
  "type": "FeatureTrack",
  "trackId": "gwas_track_parkinsons",
  "name": "GWAS Parkinsons",
  "category": ["Annotation"],
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BedTabixAdapter",
    "scoreColumn": "neg_log",
    "bedGzLocation": {
      "uri": "GCST011038_buildGRCh37.4col.tsv.gz"
    },
    "index": {
      "location": {
        "uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
      },
      "indexType": "TBI"
    }
  },
  "displays": [
    {
      "displayId": "gwas_display2",
      "type": "LinearManhattanDisplay"
    }
  ]
}


I created the index with the following command:
tabix -0 -b 2 -s 1 -S 1 -e 2 -f GCST011038_buildGRCh37.4col.tsv.gz

If you need the URL for this jbrowse2 installation for testing, I could provide it to you directly.

Thank you for the advice.

All the best,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, May 24, 2023 3:27 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmod-ajax <gmo...@li...>; Jeremiah B Reyes <jr...@un...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin


[EXTERNAL EMAIL]

Hi there, the error is saying there are two tracks with the same displayId essentially, but the displayId needs to be unique, so you can change the track config to say gwas_viewer1 and gwas_viewer2 (or any random set of unique strings)

Hope that helps!
-Colin

On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I believe I successfully configured the addition of the GWAS plugin within the config.json file.  However, when I try to load the track with the example data, I get the following error:


Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0

How would I go about troubleshooting this error? Any advice would be greatly appreciated.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

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

This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un....

Re: [Gmod-ajax] Problems installing GWAS viewer plugin

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

Hi there, the error is saying there are two tracks with the same displayId
essentially, but the displayId needs to be unique, so you can change the
track config to say gwas_viewer1 and gwas_viewer2 (or any random set of
unique strings)

Hope that helps!
-Colin

On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...>
wrote:

> Hello All,
>
> I believe I successfully configured the addition of the GWAS plugin within
> the config.json file.  However, when I try to load the track with the
> example data, I get the following error:
>
> Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0
>
> How would I go about troubleshooting this error? Any advice would be
> greatly appreciated.
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Problems installing GWAS viewer plugin

[Hans Vasquez-G. <hva...@un...>]

Hello All,

I believe I successfully configured the addition of the GWAS plugin within the config.json file.  However, when I try to load the track with the example data, I get the following error:


Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0

How would I go about troubleshooting this error? Any advice would be greatly appreciated.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

Re: [Gmod-ajax] How does jbrowse1 import bedgraph files

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

Hello,

Generally speaking, it's best to ask questions like this on the JBrowse
mailing list, cc'ed here.

I'm reasonably sure JBrowse 1 doesn't support bedGraph directly. Rather,
you have to convert it to BigWig with the UCSC tool bedGraphToBigWig, which
can be downloaded from here: http://hgdownload.soe.ucsc.edu/admin/exe/

Scott


On Wed, May 17, 2023 at 1:22 AM 137...@qq... <cho...@qq...> wrote:

> Hi, I'm asking jbrowse1 how to import a file of type bedGraph and
> configure the tracks.conf file
> Can you help me with it?Thank you very much
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] Failed to import the fasta file. Procedure

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

Hello,

Please keep the mailing list cc'ed so other people can see the thread and
offer suggestions. I gather what you want is to also have features
displayed in your JBrowse instance. To get features, they have to come from
somewhere. The most common thing would be GFF files that have the features
defined in them, but I don't know what your organism is, so I can't give
you any advice about where to find feature data.  Once you have GFF files,
you can use the script flatfile_to_json.pl to prepare it for JBrowse.

Scott


On Fri, May 12, 2023 at 12:57 AM 137...@qq... <cho...@qq...> wrote:

> hello,I zoomed in. It looks good,I use this command:./prepare-refseqs.pl
> --fasta /mnt/tomcat8/webapps/jbrowse/data/Bbraunii_502_2.0.fa,The effect is
> shown below:
> But I want it to look like this. What command should I use?I don't
> understand this very well, please give me some improvement, thank you very
> much
>
>
>
> ------------------ 原始邮件 ------------------
> *发件人:* "Scott Cain" <sc...@sc...>;
> *发送时间:* 2023年5月12日(星期五) 中午12:51
> *收件人:* "137...@qq..."<cho...@qq...>;
> *抄送:* "gmod-ajax"<gmo...@li...>;
> *主题:* Re: [Gmod-ajax] Failed to import the fasta file. Procedure
>
> 
>
> Hello,
>
> Did you zoom in? Usually, when it says “zoom in it see sequence” there is
> sequence there. If not, please send your config files and any commands you
> ran (including what directory you were in when you ran the commands).
>
> Scott
>
>
> On May 11, 2023, at 3:24 PM, 137...@qq... via Gmod-ajax <
> gmo...@li...> wrote:
>
> After installing jbrowse1 software, I want to import a fasta file, I
> follow the instructions, but nothing is displayed.
> Please help me, thank you.
> <048...@8D...g>
>
> <8B3...@AA...g>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] Failed to import the fasta file. Procedure

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



Hello, 

Did you zoom in? Usually, when it says “zoom in it see sequence” there is sequence there. If not, please send your config files and any commands you ran (including what directory you were in when you ran the commands). 

Scott


> On May 11, 2023, at 3:24 PM, 137...@qq... via Gmod-ajax <gmo...@li...> wrote:
> After installing jbrowse1 software, I want to import a fasta file, I follow the instructions, but nothing is displayed.
> Please help me, thank you.
> <048...@8D...g>
> 
> <8B3...@AA...g>
> 
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax