[Gmod-ajax] bam files outside JBrowse folder

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[Gmod-ajax] bam files outside JBrowse folder

Ke Jiang
Hi,

I wonder whether there is a way to fetch BAM files outside the JBrowse folder on the same machine. It works perfectly when use the relative path for 'urltemplate' parameter, but once that relative path goes out of JBrowse main folder it stops working and keeps looking for files under JBrowse. I know it could do http accessing remote BAMs, can it do it without http or ftp?

Thanks!

Ke

--
Ke Jiang, Ph.D. 
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724


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Re: bam files outside JBrowse folder

Ben Bimber
If they're on the same machine could you create sym links from the original file to somewhere under the jbrowse folder?  we're doing something similar to allow different databases to share resources without copying them.

-Ben


On Wed, Jul 30, 2014 at 11:40 AM, Ke Jiang <[hidden email]> wrote:
Hi,

I wonder whether there is a way to fetch BAM files outside the JBrowse folder on the same machine. It works perfectly when use the relative path for 'urltemplate' parameter, but once that relative path goes out of JBrowse main folder it stops working and keeps looking for files under JBrowse. I know it could do http accessing remote BAMs, can it do it without http or ftp?

Thanks!

Ke

--
Ke Jiang, Ph.D. 
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724


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Re: bam files outside JBrowse folder

Jillian Rowe
In reply to this post by Ke Jiang
If you are running apache you can use an alias.


 <VirtualHost #:443>
       Alias /genomes /data/share/web_public/jbrowse_ucschg19/genomes
       Alias /ucschg19 /data/share/web_public/jbrowse_ucschg19/reference_data
   </VirtualHost>

On nginx it looks like this.

    location /ucschg19
    {  
        alias /data/share/web_public/jbrowse_ucschg19;
    }  

And your tracklist.json looks like:

"urlTemplate"   : "/genomes/1000genomes/{refseq}/ALL.{refseq}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz",




On 07/30/2014 09:40 PM, Ke Jiang wrote:
Hi,

I wonder whether there is a way to fetch BAM files outside the JBrowse folder on the same machine. It works perfectly when use the relative path for 'urltemplate' parameter, but once that relative path goes out of JBrowse main folder it stops working and keeps looking for files under JBrowse. I know it could do http accessing remote BAMs, can it do it without http or ftp?

Thanks!

Ke

--
Ke Jiang, Ph.D. 
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724



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Reboot your WinForms applications with our WinForms controls. 
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk


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