Problem with plugins in GBrowse2

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Problem with plugins in GBrowse2

vstrelet

Hi,

 

I was debugging strange output of FastaDumper

plugin and realized that probably I'm using

version which was not supposed to work with

current GBrowse2.

 

Visited CPAN - list of plugins contains FastaDumper,

but it is not connected to anything submitted.

Half of the plugins are that way on that page.

 

Links from GMOD wiki (to same CPAN) produces list

of something totally unrelated.

 

Checked how plugins work on other MODs and

realized that FastaDumper does proper color

decoration only on WormBase site, on others

(FlyBase too) it just dumps completely undecorated

fasta (like txt instead of html).

 

Can somebody clarify what is the known

situation with plugins? Is it possible that

FastaDumper which comes packaged with GBrowse2

was somehow left unreplaced with current version?

It was dated 2005 coming with GBrowse2 2.54.

 

Any info will help.

 

Victor

 


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Re: Problem with plugins in GBrowse2

Lincoln Stein
The Fasta dumper that is packaged with GBrowse2 should still be working. Are you not getting HTML output at all?

Lincoln


On Tue, Apr 23, 2013 at 3:04 PM, Victor Strelets <[hidden email]> wrote:

Hi,

 

I was debugging strange output of FastaDumper

plugin and realized that probably I'm using

version which was not supposed to work with

current GBrowse2.

 

Visited CPAN - list of plugins contains FastaDumper,

but it is not connected to anything submitted.

Half of the plugins are that way on that page.

 

Links from GMOD wiki (to same CPAN) produces list

of something totally unrelated.

 

Checked how plugins work on other MODs and

realized that FastaDumper does proper color

decoration only on WormBase site, on others

(FlyBase too) it just dumps completely undecorated

fasta (like txt instead of html).

 

Can somebody clarify what is the known

situation with plugins? Is it possible that

FastaDumper which comes packaged with GBrowse2

was somehow left unreplaced with current version?

It was dated 2005 coming with GBrowse2 2.54.

 

Any info will help.

 

Victor

 


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Problem with plugins in GBrowse2

Walter, Mathias
Hi,

it works great with my 2.54 installation.

--
Regards,
Mathias

2013/4/23 Lincoln Stein <[hidden email]>:

> The Fasta dumper that is packaged with GBrowse2 should still be working. Are
> you not getting HTML output at all?
>
> Lincoln
>
>
> On Tue, Apr 23, 2013 at 3:04 PM, Victor Strelets
> <[hidden email]> wrote:
>>
>> Hi,
>>
>>
>>
>> I was debugging strange output of FastaDumper
>>
>> plugin and realized that probably I'm using
>>
>> version which was not supposed to work with
>>
>> current GBrowse2.
>>
>>
>>
>> Visited CPAN - list of plugins contains FastaDumper,
>>
>> but it is not connected to anything submitted.
>>
>> Half of the plugins are that way on that page.
>>
>>
>>
>> Links from GMOD wiki (to same CPAN) produces list
>>
>> of something totally unrelated.
>>
>>
>>
>> Checked how plugins work on other MODs and
>>
>> realized that FastaDumper does proper color
>>
>> decoration only on WormBase site, on others
>>
>> (FlyBase too) it just dumps completely undecorated
>>
>> fasta (like txt instead of html).
>>
>>
>>
>> Can somebody clarify what is the known
>>
>> situation with plugins? Is it possible that
>>
>> FastaDumper which comes packaged with GBrowse2
>>
>> was somehow left unreplaced with current version?
>>
>> It was dated 2005 coming with GBrowse2 2.54.
>>
>>
>>
>> Any info will help.
>>
>>
>>
>> Victor
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Try New Relic Now & We'll Send You this Cool Shirt
>> New Relic is the only SaaS-based application performance monitoring
>> service
>> that delivers powerful full stack analytics. Optimize and monitor your
>> browser, app, & servers with just a few lines of code. Try New Relic
>> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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Re: Problem with plugins in GBrowse2

vstrelet
In reply to this post by Lincoln Stein

On Tuesday, April 23, 2013 04:05:37 PM Lincoln Stein wrote:

> The Fasta dumper that is packaged with GBrowse2 should still be working.

> Are you not getting HTML output at all?

 

I'm getting thing which is in fact HTML, but nothing

on page is decorated in any way. Any changes to

configuration (what to color etc.) appear to be

remembered, but no action is visible, and debugging

tells me that it simply fails to retrieve features

through iterator.

 

It might be a problem with particular adaptor and

I'm preparing to rework some things in it (iterator

and type of features it returns to browser), but

I'm trying to make sure that there is no known

problem in this area.

 

Confusing is that same "will not decorate"

behavior I can see on other GBrowse2 installations,

for example, on ParameciumDB.

 

On SGD, it fails to show config for dumper at all.

 

MGI doesn't even show that dumper as a choice

althought it is a default in distributed GBrowse.conf

 

Victor

 


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Re: Problem with plugins in GBrowse2

Siddhartha Basu
Hi,

On Tue, 23 Apr 2013, Victor Strelets wrote:

>    On Tuesday, April 23, 2013 04:05:37 PM Lincoln Stein wrote:
>
>    > The Fasta dumper that is packaged with GBrowse2 should still be working.
>
>    > Are you not getting HTML output at all?
>
>    
>
>    I'm getting thing which is in fact HTML, but nothing
>
>    on page is decorated in any way. Any changes to
>
>    configuration (what to color etc.) appear to be
>
>    remembered, but no action is visible, and debugging
>
>    tells me that it simply fails to retrieve features
>
>    through iterator.
>
>    
>
>    It might be a problem with particular adaptor and
>
>    I'm preparing to rework some things in it (iterator
>
>    and type of features it returns to browser), but
>
>    I'm trying to make sure that there is no known
>
>    problem in this area.

I had similar kind of issue at dictyBase with gb 2.40. The plugin was
not decorating sequences from multiple tracks rather was picking up a
single one. So, there were no multiplexing of colors.
The problem turns out be coming from tracks that are
from different datasources. For us it was the tracks that comes from
different postgresql schemas(same database different namespaces in terms
of Bio::DB::SeqFeature::Store convention)
The solution was to get an array of features instead of the iterator.
The patch/change is here ...
https://github.com/dictyBase/GBrowse-PSGI/commit/02d86e48419646d33ca038b820ed1dbaae4772c5
The 'get_seq_stream' method also seems to use an undocumented argument
(-automerge => 1)
https://metacpan.org/module/Bio::DB::SeqFeature::Segment#get_seq_stream

Our curators have tested it with their workflow and
now the decorations seems to work reasonably well with all the tracks.
The behaviour is also consistent with previous gbrowse version(v1).
However, tracks from *bam* datasource will not decorate, probably this
is an expected behaviour, but i am not sure  and haven't dug enough on
it.



>
>    
>
>    Confusing is that same "will not decorate"
>
>    behavior I can see on other GBrowse2 installations,
>
>    for example, on ParameciumDB.
>
>    
>
>    On SGD, it fails to show config for dumper at all.
>
>    
>
>    MGI doesn't even show that dumper as a choice
>
>    althought it is a default in distributed GBrowse.conf
>
>    
It works at dictyBase now and you might give it a try and check if
this is the behavior you are expecting.
http://dictybase.org/browser/gbrowse/discoideum/?name=3:1..30000

Hope this helps,
thanks,
-siddhartha



>
>    Victor
>
>    

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