[Gmod-ajax] Jbrowse and http access to BAM files

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[Gmod-ajax] Jbrowse and http access to BAM files

Keiran Raine
Hi,

I'm just getting started working with JBrowse and I seem to have hit a problem when accessing BAM tracks via URL on JBrowse 1.10.1.

I've attempted to do this both via the browser upload and as a pre-defined track both giving the same error:


In the browser I specify both:

http://myhost/file/dev_812/PD4107a.bwa.bam.bai

and it offers a sensible track name and appears to generate the relevant track for selection, but when you attempt to access the above error is given.

Definition in trackList.json:

{
   "storeClass" : "JBrowse/Store/SeqFeature/BAM",
   "urlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam",
   "baiUrlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam.bai",
   "type" : "JBrowse/View/Track/Alignments2",
   "label" : "PD4107a BWA",
   "key" : "PD4107a BWA"
}

This again seems to work until you actually attempt to view the track.  Setup doesn't seem to have thrown any errors (setup.log attached).

I know that my file server is working as it is fine for GBrowse and via the command line requests such as:

> samtools view http://myhost/file/dev_812/PD4107a.bwa.bam 1:1-1
[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.
[bam_index_load] attempting to download the remote index file.
[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.

Hopefully someone can shed some light on this for me.

Rind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.


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Re: Jbrowse and http access to BAM files

Robert Buels-2
Hi Keiran,

Sorry for the slow response, I've been on vacation.

Are you still having this problem?  If those URLs work for samtools,
then the most likely source of problems with this configuration would be
the JavaScript same-origin policy, which requires that the web server
that's serving the files either a.) be the same as the one serving
JBrowse, or b.) supports CORS and is configured to allow the URL with
JBrowse to access them.  For more on CORS, and how to enable it, see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Cross-origin_resource_sharing_.28CORS.29:_showing_data_on_multiple_servers


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 08/19/2013 12:38 PM, Keiran Raine wrote:

> Hi,
>
> I'm just getting started working with JBrowse and I seem to have hit a
> problem when accessing BAM tracks via URL on JBrowse 1.10.1.
>
> I've attempted to do this both via the browser upload and as a
> pre-defined track both giving the same error:
>
> Unable to fetch http://myhost/file/dev_812/PD4107a.bwa.bam
>
> In the browser I specify both:
>
> http://myhost/file/dev_812/PD4107a.bwa.bam
> http://myhost/file/dev_812/PD4107a.bwa.bam.bai
>
> and it offers a sensible track name and appears to generate the relevant
> track for selection, but when you attempt to access the above error is
> given.
>
> Definition in trackList.json:
>
> {
>     "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>     "urlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam",
>     "baiUrlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam.bai",
>     "type" : "JBrowse/View/Track/Alignments2",
>     "label" : "PD4107a BWA",
>     "key" : "PD4107a BWA"
> }
>
> This again seems to work until you actually attempt to view the track.
>   Setup doesn't seem to have thrown any errors (setup.log attached).
>
> I know that my file server is working as it is fine for GBrowse and via
> the command line requests such as:
>
>  > samtools view http://myhost/file/dev_812/PD4107a.bwa.bam 1:1-1
> [knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.
> [bam_index_load] attempting to download the remote index file.
>  > samtools view http://myhost/file/dev_812/PD4107a.bwa.bam 1:1-1
> [knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.
>
> Hopefully someone can shed some light on this for me.
>
> Rind regards,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Rese arch
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
>
>
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
> Visit us today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: Jbrowse and http access to BAM files

Keiran Raine
Hi Robert,

Thanks, that explains it.  I've found under GBrowse that http access is not really suitable for a large number of datasources so for now switched back to direct file access while I get the hang of this.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 28 Aug 2013, at 15:14, Robert Buels <[hidden email]> wrote:

Hi Keiran,

Sorry for the slow response, I've been on vacation.

Are you still having this problem?  If those URLs work for samtools, then the most likely source of problems with this configuration would be the JavaScript same-origin policy, which requires that the web server that's serving the files either a.) be the same as the one serving JBrowse, or b.) supports CORS and is configured to allow the URL with JBrowse to access them.  For more on CORS, and how to enable it, see http://gmod.org/wiki/JBrowse_Configuration_Guide#Cross-origin_resource_sharing_.28CORS.29:_showing_data_on_multiple_servers


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 08/19/2013 12:38 PM, Keiran Raine wrote:
Hi,

I'm just getting started working with JBrowse and I seem to have hit a
problem when accessing BAM tracks via URL on JBrowse 1.10.1.

I've attempted to do this both via the browser upload and as a
pre-defined track both giving the same error:

Unable to fetch http://myhost/file/dev_812/PD4107a.bwa.bam

In the browser I specify both:

http://myhost/file/dev_812/PD4107a.bwa.bam
http://myhost/file/dev_812/PD4107a.bwa.bam.bai

and it offers a sensible track name and appears to generate the relevant
track for selection, but when you attempt to access the above error is
given.

Definition in trackList.json:

{
   "storeClass" : "JBrowse/Store/SeqFeature/BAM",
   "urlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam",
   "baiUrlTemplate" : "http://myhost/file/dev_812/PD4107a.bwa.bam.bai",
   "type" : "JBrowse/View/Track/Alignments2",
   "label" : "PD4107a BWA",
   "key" : "PD4107a BWA"
}

This again seems to work until you actually attempt to view the track.
 Setup doesn't seem to have thrown any errors (setup.log attached).

I know that my file server is working as it is fine for GBrowse and via
the command line requests such as:

> samtools view http://myhost/file/dev_812/PD4107a.bwa.bam 1:1-1
[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.
[bam_index_load] attempting to download the remote index file.
> samtools view http://myhost/file/dev_812/PD4107a.bwa.bam 1:1-1
[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.

Hopefully someone can shed some light on this for me.

Rind regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger institute

[hidden email] <mailto:[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.




------------------------------------------------------------------------------
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk



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-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
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