gmod-ajax — JBrowse list

Re: [Gmod-ajax] error installing Jbrowse

[James C. <ca...@gm...>]

On 31 October 2011 16:09, Radhouane Aniba <ar...@gm...> wrote:
> Hello everyone
>
> I am trying to install Jbrowse but I am not able to compile wig2png, I am
> running under Ubuntu and have this error message after make command
>
> g++ -g -O2 -include src/config.h  -lpng  -o bin/wig2png src/wig2png.cc

gcc4.6 is messing with all my builds - what are you using?

[Gmod-ajax] error installing Jbrowse

[Radhouane A. <ar...@gm...>]

Hello everyone

I am trying to install Jbrowse but I am not able to compile wig2png, I am
running under Ubuntu and have this error message after make command

g++ -g -O2 -include src/config.h  -lpng  -o bin/wig2png src/wig2png.cc
src/opts_list.cc
/tmp/ccuLlP8o.o: In function `write_png_file(char const*, int, int,
unsigned char**, png_color_struct*, int, int)':
/var/www/jbrowse/src/wig2png.cc:46: undefined reference to
`png_create_write_struct'
/var/www/jbrowse/src/wig2png.cc:52: undefined reference to
`png_create_info_struct'
/var/www/jbrowse/src/wig2png.cc:65: undefined reference to `png_init_io'
/var/www/jbrowse/src/wig2png.cc:70: undefined reference to `png_set_IHDR'
/var/www/jbrowse/src/wig2png.cc:73: undefined reference to `png_set_PLTE'
/var/www/jbrowse/src/wig2png.cc:76: undefined reference to `png_set_rows'
/var/www/jbrowse/src/wig2png.cc:80: undefined reference to `png_set_filter'
/var/www/jbrowse/src/wig2png.cc:81: undefined reference to
`png_set_compression_level'
/var/www/jbrowse/src/wig2png.cc:85: undefined reference to `png_write_png'
/var/www/jbrowse/src/wig2png.cc:87: undefined reference to
`png_destroy_write_struct'
/var/www/jbrowse/src/wig2png.cc:60: undefined reference to
`png_destroy_write_struct'
/var/www/jbrowse/src/wig2png.cc:54: undefined reference to
`png_destroy_write_struct'
collect2: ld returned 1 exit status
make: *** [bin/wig2png] Error 1

Any idea ? Am I missing something ?

Once we succeed to do this, it is not clear in the documentation which
folder will contain the data once processed and how to view the result,
quite confusing

Thanks for the help

Rad

--

Re: [Gmod-ajax] Display a track in the View window by default

[Philippe S. <soa...@gm...>]

Hi,
You can define the names of the tracks in the "tracks" parameter in the URL.
Your example would be : 
http://www.genomesunzipped.org/jbrowse?tracks=Transcript,SNPs

Regards,

Philippe

Le 24/10/11 19:08, Nguyen, Anh-Dao (NIH/NHGRI) [C] a écrit :
> Hi,
>
> How can I display a specific track in the View window by default when the JBrowse page is loaded.
> For instance, the RefSeq genes and 23andMe SNPs tracks on the page http://www.genomesunzipped.org/jbrowse/
>
> Thanks
>
> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn
> about Cisco certifications, training, and career opportunities.
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[Gmod-ajax] Display a track in the View window by default

[Nguyen, Anh-D. (NIH/N. [C] <ngu...@ma...>]

Hi,

How can I display a specific track in the View window by default when the JBrowse page is loaded.
For instance, the RefSeq genes and 23andMe SNPs tracks on the page http://www.genomesunzipped.org/jbrowse/

Thanks

Re: [Gmod-ajax] Monthly JBrowse developers conference call

[Suzanna L. <su...@be...>]

Lincoln and/or Natalie,

It would be great to hear something on the faceted browser index for JBrowse. Chris Childers at Georgetown has been doing some work on it as well.

-S

On Oct 14, 2011, at 8:52 AM, Ian Holmes wrote:

> The monthly JBrowse developers' conference call will be on Monday
> October 17th (3rd Monday of the month) at 2pm.
> 
> Call details:
> 
> 1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
> (The toll-free number from Thailand is 001800656911)
> 2. Enter access code 4867508#
> 
> Please feel free to join,
> 
> Best wishes
> Ian
> 
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] Monthly JBrowse developers conference call

[Ian H. <ihh...@gm...>]

The monthly JBrowse developers' conference call will be on Monday
October 17th (3rd Monday of the month) at 2pm.

Call details:

1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
(The toll-free number from Thailand is 001800656911)
2. Enter access code 4867508#

Please feel free to join,

Best wishes
Ian

[Gmod-ajax] How to highlight features in a specific genomic region in JBrowse?

[Fengyuan Hu <fh...@ca...>]

Hi JBrowse developers,

Thanks for bringing us this excellent tool.

I started to use JBrowse a couple of days ago, I tried to figure out how 
to highlight feature names of certain tracks within a specified region 
by javascript (e.g. highlight names of genes, transcripts and SNPs in 
human chr1:100000-2000000), but I couldn't find an answer from the 
documents, could anyone point me out, please?

Thanks
Fengyuan

Re: [Gmod-ajax] JBrowse conference call, September 19th, 2pm Pacific

[Ian H. <ihh...@gm...>]

Thanks Martin, we will certainly do this once we have finished the process of hiring someone to do the developing. Prioritized requests from the community are an excellent idea. An even higher priority is integrating contributions of code developed *by* the community. We plan to do both, soon.

-Ian

On Sep 21, 2011, at 5:08 AM, Martin Asser Hansen <ma...@ma...> wrote:

> Hello Ian et al.,
> 
> 
> May I suggest to disclose the development plans of Jbrowse including a prioritized list of feature requests from the community. To me, Jbrowse is not quite ripe, and certain features are badly missing - like easy hosting of multiple genomes and managing custom tracks from a setup perspective. I think these issues are more important than the ability of Jbrowse to run on an Ipad :o). I also think it is important for the Jbrowse project to be in sync with the wishes of users.
> 
> 
> 
> Cheers,
> 
> 
> Martin Asser Hansen
> Cand. Scient., PhD
> 
> Postdoctoral Fellow
> Molecular Microbial Ecology Group
> University of Copenhagen
> Sølvgade 83H
> DK-1307K
> DENMARK
> 
> E-mail:  ma...@ma...
> Skype:   martinasserhansen
> Website: www.maasha.dk
> Mobile:  +45 60722228
> 
> On Tue, Aug 30, 2011 at 12:09 AM, Ian Holmes <ihh...@gm...> wrote:
> Hello JBrowse users and developers,
> 
> The first JBrowse developers' conference call will be held on Sept 19
> at 2pm Pacific time. We intend for this to be a monthly event. Call
> details are below; we hope you will join in.
> 
> The main agenda topics for this first call will be:
> - Introductions; quick survey of projects built on, or with, JBrowse
> - JBrowse funding situation
> - JBrowse software developments
> - JBrowse and Web-Apollo
> - Any other business
> 
> Please email me if there is anything you'd like to have on the agenda.
> 
> Call details:
> 
> 1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
> (The toll-free number from Thailand is 001800656911)
> 2. Enter access code 4867508#
> 
> 
> Best wishes
> Ian
> 
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse conference call, September 19th, 2pm Pacific

[Martin A. H. <ma...@ma...>]

Hello Ian et al.,


May I suggest to disclose the development plans of Jbrowse including a
prioritized list of feature requests from the community. To me, Jbrowse is
not quite ripe, and certain features are badly missing - like easy hosting
of multiple genomes and managing custom tracks from a setup perspective. I
think these issues are more important than the ability of Jbrowse to run on
an Ipad :o). I also think it is important for the Jbrowse project to be in
sync with the wishes of users.



Cheers,


Martin Asser Hansen
Cand. Scient., PhD

Postdoctoral Fellow
Molecular Microbial Ecology Group
University of Copenhagen
Sølvgade 83H
DK-1307K
DENMARK

E-mail:  ma...@ma...
Skype:   martinasserhansen
Website: www.maasha.dk
Mobile:  +45 60722228

On Tue, Aug 30, 2011 at 12:09 AM, Ian Holmes <ihh...@gm...> wrote:

> Hello JBrowse users and developers,
>
> The first JBrowse developers' conference call will be held on Sept 19
> at 2pm Pacific time. We intend for this to be a monthly event. Call
> details are below; we hope you will join in.
>
> The main agenda topics for this first call will be:
> - Introductions; quick survey of projects built on, or with, JBrowse
> - JBrowse funding situation
> - JBrowse software developments
> - JBrowse and Web-Apollo
> - Any other business
>
> Please email me if there is anything you'd like to have on the agenda.
>
> Call details:
>
> 1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
> (The toll-free number from Thailand is 001800656911)
> 2. Enter access code 4867508#
>
>
> Best wishes
> Ian
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: Jbrowse question

[Ian H. <ihh...@gm...>]

Terry,

I suspect the "Use of uninitialized value.." error was indeed a
missing command-line argument (possibly --tracklabel), but the fact
that you get the segfault even when all cmd-line args are specified
suggests that this isn't the root cause.

In fact, from your tracing of the segfault to that line, it seems to
be happening in the 'fetch' method of the Bio::DB::Bam index, which is
a module external to jbrowse and (I fear) not something we can easily
help with.

At this point I would probably recommend
(a) updating your Bio-SamTools to the latest version, if applicable
(and if that fails, maybe even doing a clean install of your Perl
infrastructure from scratch)
(b) attempting to figure out exactly what is being passed to
Bio::DB::Bam, reproducing the error outside of jbrowse, and taking it
to the appropriate Bio-SamTools mailing list.

I suspect our cloud image will not be much help as it has not yet been
updated to include the bam-to-json script or associated Perl modules.
However, if you install those things & update jbrowse, it might work.

Sorry I can't be more help...
Ian

On Wed, Sep 14, 2011 at 7:07 AM, Terry Camerlengo
<ter...@gm...> wrote:
> BTW - this is the line that seems to be giving me the
> trouble/segmentation fault.
>
>        $index->fetch($bam, $tid, $start, $end,
>                      sub { $sorter->addSorted(align2array($_[0])) });
>
> Any recommendations on how to troubleshoot this?
>
> Thanks.
>
> Terry
>
> On Tue, Sep 13, 2011 at 2:58 PM, Ian Holmes <ihh...@gm...> wrote:
>> Terry, please see Seth's suggestion below. The problem may lie in JSON::XS.
>> Please let us know how you get on.
>> Thanks, Ian
>>
>> ---------- Forwarded message ----------
>> From: Seth Carbon <sjc...@lb...>
>> Date: Mon, Sep 12, 2011 at 7:54 PM
>> Subject: Re: [Gmod-ajax] Fwd: Jbrowse question
>>
>>> From: Terry Camerlengo <ter...@gm...>
>>> Date: Mon, Sep 12, 2011 at 5:58 PM
>>> Subject: RE: Jbrowse question
>>>
>>>
>>> To the JBrowse team:
>>>
>>> I have been trying to get JBrowse included as part of our groups core NGS image.
>>> We are using Solid/Lifescope to generate bam files and so I am working
>>> with the bam-to-json.pl script. I am running Centos 5.6 and the
>>> tutorial works for me (except the bam file part of course). If I run
>>> the bam-to-json script with no params I am getting the help display.
>>> (I assume this means I have all of the library prerequisites.) Then I
>>> run the following...
>>>
>>>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam (The index file is in the same directory with the same base name)
>>>
>>> and I get  the following message:
>>>
>>> "Use of uninitialized value in concatenation (.) or string at
>>> bin/bam-to-json.pl line 91."
>>>
>>> followed by a Segmentation Fault.
>>>
>>> Then I run the following thinking it has something to do with a
>>> missing parameter..
>>>
>>>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam  --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
>>>
>>> And I just get the Segmentation Fault.
>>
>> Ian,
>>
>> This is somewhat similar to a JSON module problem I had with perl a
>> while ago--it turned out that the JSON::XS module had issues with really
>> big ints and would segfault. Since the JSON module will automatically
>> use JSON::XS if available, and fall back to JSON::PP if it's not, you
>> can test for this by forcing the choice and removing JSON::XS from your
>> system.
>>
>> I thought it sounded familiar and might be worth a try.
>>
>> Cheers,
>>
>> -Seth
>>
>>
>>> An online search provided nothing useful and I am not sure what the
>>> problem could be. This is a general .bam file used for testing and is
>>> valid. Is there anyway to trouble shoot this? Does JBrowse log error
>>> info someplace? Is there a verbose setting for bam-to-json? Am I
>>> messing up the command line?
>>>
>>> Thanks.
>>>
>>> ------------------------------------------------------------------------------
>>> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
>>> Learn about the latest advances in developing for the
>>> BlackBerry&reg; mobile platform with sessions, labs & more.
>>> See new tools and technologies. Register for BlackBerry&reg; DevCon today!
>>> http://p.sf.net/sfu/rim-devcon-copy1
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>

[Gmod-ajax] Fwd: Fwd: Jbrowse question

[Ian H. <ihh...@gm...>]

Terry, please see Seth's suggestion below. The problem may lie in JSON::XS.
Please let us know how you get on.
Thanks, Ian

---------- Forwarded message ----------
From: Seth Carbon <sjc...@lb...>
Date: Mon, Sep 12, 2011 at 7:54 PM
Subject: Re: [Gmod-ajax] Fwd: Jbrowse question

> From: Terry Camerlengo <ter...@gm...>
> Date: Mon, Sep 12, 2011 at 5:58 PM
> Subject: RE: Jbrowse question
>
>
> To the JBrowse team:
>
> I have been trying to get JBrowse included as part of our groups core NGS image.
> We are using Solid/Lifescope to generate bam files and so I am working
> with the bam-to-json.pl script. I am running Centos 5.6 and the
> tutorial works for me (except the bam file part of course). If I run
> the bam-to-json script with no params I am getting the help display.
> (I assume this means I have all of the library prerequisites.) Then I
> run the following...
>
>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam (The index file is in the same directory with the same base name)
>
> and I get  the following message:
>
> "Use of uninitialized value in concatenation (.) or string at
> bin/bam-to-json.pl line 91."
>
> followed by a Segmentation Fault.
>
> Then I run the following thinking it has something to do with a
> missing parameter..
>
>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam  --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
>
> And I just get the Segmentation Fault.

Ian,

This is somewhat similar to a JSON module problem I had with perl a
while ago--it turned out that the JSON::XS module had issues with really
big ints and would segfault. Since the JSON module will automatically
use JSON::XS if available, and fall back to JSON::PP if it's not, you
can test for this by forcing the choice and removing JSON::XS from your
system.

I thought it sounded familiar and might be worth a try.

Cheers,

-Seth


> An online search provided nothing useful and I am not sure what the
> problem could be. This is a general .bam file used for testing and is
> valid. Is there anyway to trouble shoot this? Does JBrowse log error
> info someplace? Is there a verbose setting for bam-to-json? Am I
> messing up the command line?
>
> Thanks.
>
> ------------------------------------------------------------------------------
> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
> Learn about the latest advances in developing for the
> BlackBerry&reg; mobile platform with sessions, labs & more.
> See new tools and technologies. Register for BlackBerry&reg; DevCon today!
> http://p.sf.net/sfu/rim-devcon-copy1
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Fwd: Jbrowse question

[Ian H. <ihh...@gm...>]

---------- Forwarded message ----------
From: Terry Camerlengo <ter...@gm...>
Date: Mon, Sep 12, 2011 at 5:58 PM
Subject: RE: Jbrowse question
To: mit...@be..., ih...@be...


To the JBrowse team:

I have been trying to get JBrowse included as part of our groups core NGS image.
We are using Solid/Lifescope to generate bam files and so I am working
with the bam-to-json.pl script. I am running Centos 5.6 and the
tutorial works for me (except the bam file part of course). If I run
the bam-to-json script with no params I am getting the help display.
(I assume this means I have all of the library prerequisites.) Then I
run the following...

>>bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam (The index file is in the same directory with the same base name)

and I get  the following message:

"Use of uninitialized value in concatenation (.) or string at
bin/bam-to-json.pl line 91."

followed by a Segmentation Fault.

Then I run the following thinking it has something to do with a
missing parameter..

>>bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam  --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'

And I just get the Segmentation Fault.

An online search provided nothing useful and I am not sure what the
problem could be. This is a general .bam file used for testing and is
valid. Is there anyway to trouble shoot this? Does JBrowse log error
info someplace? Is there a verbose setting for bam-to-json? Am I
messing up the command line?

Thanks.

[Gmod-ajax] Early registration for October GMOD meeting closing

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

Hello,

The early registration deadline for the October GMOD meeting in
Toronto, Canada is approaching.  Please register by September 13th to
avoid the late registration fee.  You can register here:

  http://gmod.eventbrite.com/

For information about the GMOD meeting please see the page at:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

In addition to the main meeting, there will be a free BioMart workshop
on the following Friday, which you can also register for at the main
meeting registration page.

Thanks,
Scott


-- 
------------------------------------------------------------------------
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 conference call, September 19th, 2pm Pacific

[Ian H. <ihh...@gm...>]

Hello JBrowse users and developers,

The first JBrowse developers' conference call will be held on Sept 19
at 2pm Pacific time. We intend for this to be a monthly event. Call
details are below; we hope you will join in.

The main agenda topics for this first call will be:
- Introductions; quick survey of projects built on, or with, JBrowse
- JBrowse funding situation
- JBrowse software developments
- JBrowse and Web-Apollo
- Any other business

Please email me if there is anything you'd like to have on the agenda.

Call details:

1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
(The toll-free number from Thailand is 001800656911)
2. Enter access code 4867508#


Best wishes
Ian

[Gmod-ajax] Toronto GMOD meeting registration now open

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

Hello,

I am pleased to announce that registration is now open for the October
12-13 GMOD meeting at OICR in Toronto, Canada.  Please visit the
registration site at:

  http://gmod.eventbrite.com/

The registration fee for the meeting is $40 if registered before
September 13.  After September 13, the registration fee goes up to
$50.  For more information about the meeting, including information on
our excellent keynote speakers, Gary Bader and Michael Brudno, please
visit the meeting page:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

While at the meeting page, please make sure to suggest topics, talks
and satellites for the meeting.

I look forward to seeing you in Toronto!
Scott



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

[Gmod-ajax] GMOD Community Meeting October 12-13, Toronto

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

Hello,

I am pleased to formally announce pre-registration for the upcoming
GMOD community meeting which will take place October 12-13 in Toronto,
Ontario, Canada, hosted by the Ontario Institute for Cancer Research.
The meeting web page is here:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

and while it is still under construction, the registration page should
be available by the end of next week, along with information about the
keynote speaker(s) and logistics like hotels.  In the mean time, I
urge you to go to the meeting page and add suggested topics and talks
to the appropriate section.

Finally, the meeting itself will be limited in size, so when
registration is open, I urge you to register as soon as possible,
since I may need to close registration when we are full.

Thanks and I look forward to seeing you in Toronto,
Scott


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

[Gmod-ajax] GFF files in Jbrowse

[Diego O. D. V. <die...@uc...>]

To whom it may concern,

I am using Jbrowse to set up a local genome browser with data we are  
generating in our lab. I have a couple of questions regarding how to  
use Jbrowse:

1) I have a GFF3 file which has data listed in the following way:

chr01	.	GENE	3692374	3703202	.	-	.	ID=606936;Name=LOC606936
chr01	.	RNA	3692374	3703202	.	-	.	ID=37;Parent=606936
chr01	.	UTR	3692374	3692801	.	-	.	ID=38;Parent=606936
chr01	.	CDS	3692802	3693135	.	-	.	ID=39;Parent=606936
chr01	.	CDS	3694398	3694471	.	-	.	ID=40;Parent=606936
chr01	.	CDS	3699377	3699461	.	-	.	ID=41;Parent=606936
chr01	.	CDS	3702407	3702519	.	-	.	ID=42;Parent=606936
chr01	.	CDS	3703026	3703202	.	-	.	ID=43;Parent=606936

My question is: What features do I need to add in the command line  
when I am running the script flatfile-to-json.pl to display the  
information from the category "Parent" of the features RNA, UTR and  
CDS in the Genome Browser?
Another related question is: How can I put an URL on every gene, UTR,  
RNA or CDS of the GFF3 file such that every time I click on those  
things in the genome browser, I can be directed to a database (Such as  
the FlyBase).

Thank you very much,
Diego Ortega Del Vecchyo

[Gmod-ajax] Color features accoring to score field in BED file

[Pascal G. <pas...@mp...>]

Hi,

BED files contain a score value as fifth column. Is it possible to use 
this score to color the features in JBrowse according to this score.
This might be straight forward, but I could find any instruction/example 
on this.

Thanks in advance,

Pascal

[Gmod-ajax] Seems to be a missing feature

[Gustavo C. <gu...@br...>]

Is this a missing feature? Or I'm doing something wrong
There is no scale on the wig track. And theres is no way to figure out the
coverage value (mouse over usually).
Thank you very much.

-- 
Gustavo C. Cerqueira, PhD
Bioinformatics Scientist
Broad Institute
320 Charles Street - Office 2184
Phone: (617) 714-8469
E-mail: gu...@br...

[Gmod-ajax] Where do I find documentation for urlTemplate?

[Marc C. <mr...@gm...>]

Hello everyone,

After looking at the docs, searching for the docs online etc. I cannot
find a good explanation for how to use the  --urlTemplate argument for
flatfile-to-json.pl in JBrowse.  A usage statement would be really
great for example.  There is apparently also a config file that can be
set up to use this as well, but I have been unable to locate any
examples of how to make use of one of those either.  My best guess is
that you guys have better docs somewhere and that I just have just not
found the right place?  Also, is this mailing list on GMANE or
somewhere else that would make it searchable?  I hate to be another
newbie coming in here and asking questions that have been asked a
dozen times before.

Any help would be greatly appreciated.  Thanks in advance for your
consideration,


  Marc

[Gmod-ajax] JBrowse: wiggle track resolution and track label position

[Erik D. <da...@sc...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi all,<br>
I was wondering if there is any way to solve the problem of wiggle
tracks appearing pixellated and low resolution when zooming down to
base level. Is there any way to generate more definite track images,
maybe by tweaking wig2png ?<br>
<br>
I also would like to know how can I move the track label so that it
won't overlap a feature annotated at the beginning of my sequence. Is
there a configuration option/css property I can change to do that ?<br>
<br>
thank you very much,<br>
Erik Dassi<br>
<div class="moz-signature">-- <br>
<span
 style="font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 10px; color: rgb(102, 102, 102);">Erik
Dassi<br>
PhD Student<br>
Laboratory of Translational Genomics<br>
CIBIO - Center for Integrative Biology<br>
Via delle Regole, 101<br>
38123 MATTARELLO (TN)<br>
Italy</span><br>
</div>
</body>
</html>

[Gmod-ajax] jbrowse performance on many contigs, and displaying a few genomes

[John S. J. <js...@so...>]

Hello,

Two questions:

1. I wanted to use jbrowse as a quick way to visualize a genome assembly
I am working on. I have several assemblies, each of which has around
200-400k scaffolds and are around 2GB in length. Following the tutorial
example `bin/prepare-refseqs.pl --fasta` creates a data directory with
400k sub folders and the browser takes minutes to load (if it doesn't
crash). I imagine this is because no index is stored over the sequences
so they are enumerated each time the browser is opened. Is there any way
to make jBrowse work with this kind of data? I was searching for ways to
use jbrowse with a sqlite3 backend (since getting mysql permissions
would be difficult) but couldn't find anything.

2. Since I could have a few genomes that I want to visualize at any
given time, is there a way to get jbrowse to have a heirarchial
organization over first genomes and next sequenes within the chosen
genome? Or should I just check out multiple jbrowse instances into
folders named for each genome and link to them that way?


Thanks for your help!


-John

Re: [Gmod-ajax] Error with bam-to-json.pl

[Ian H. <ih...@be...>]

Chris,

That line of the code is

     my $histBinThresh = ($self->{refEnd} * 2.5) / $self->{count};

The division by zero error suggests that it's not picking up any 
features for some reason? A workaround might be to change it to

     my $histBinThresh = ($self->{refEnd} * 2.5) / ($self->{count} || 1);

However if no features are getting picked up, this might not help. Can 
you post the BAM file somewhere I can download it?

I.


On 5/4/11 12:39 PM, Chris Childers wrote:
> Hi all,
>
> I was trying to load BAM data using JBrowse 1.2.1, and I ran into the
> following error.
>
> Illegal division by zero at
> /var/www/html/jbrowse/bin/../lib/JsonGenerator.pm line 291.
>
> I have tried this with the default BAM and with a sorted, indexed
> version of the file.  Has anyone seen this error before?
> Thanks,
> Chris
> --
> Chris Childers
> Postdoctoral Fellow
> Elsik Computational Genomics Laboratory
> Georgetown University
> Department of Biology
> 406 Reiss Bldg
> Washington, DC 20057
>
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
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>
>
>
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[Gmod-ajax] Error with bam-to-json.pl

[Chris C. <gen...@gm...>]

Hi all,

I was trying to load BAM data using JBrowse 1.2.1, and I ran into the
following error.

Illegal division by zero at
/var/www/html/jbrowse/bin/../lib/JsonGenerator.pm line 291.

I have tried this with the default BAM and with a sorted, indexed version of
the file.  Has anyone seen this error before?
Thanks,
Chris
-- 
Chris Childers
Postdoctoral Fellow
Elsik Computational Genomics Laboratory
Georgetown University
Department of Biology
406 Reiss Bldg
Washington, DC 20057

[Gmod-ajax] Problems With bam-to-json.pl

[David N. <hil...@gm...>]

I was able to resolve the issue with the wig files by recompiling wig2png
and running the wig-to-json.pl script again for each wig file.  I'm not sure
why this resolved the issue, but I can see my files now!