[Iplant-api-dev] loading iRODS data into the browser

[Cornel Ghiban]

Hi Roger,

Well, I was thinking to save some time (and disk space) and stream the bam 
files from iRODS to IGV via a perl script, but it looks like IGV requests 
use Range headers and it wants slices of the BAM file. I don't think my perl 
script will be able to handle this :)

Thanks,
Cornel

On 8/28/2012 5:15 PM, Barthelson, Roger A - (rogerab) wrote:
> Hi Cornel-
>
> I assume you mean that you have a running instance of IGV, and you want to
> move BAM files into it. Normally you would want to use icommands or
> similar to move the files into place before you start, but if that is not
> possible for what you are doing, then it seems like maybe you would need
> to have a separate thread run to move the files into place. I doubt there
> is a way of having, for example, IGV address iRods directly. Maybe there
> is somewhere, but I haven't heard of it. So, I think you have to move the
> files into place with a different thread and then open them from IGV. I'm
> not sure how that would work. I found this mysterious perl script
> recently, maybe it could help.
>
> Roger
>
>
> Roger Barthelson Ph.D.
> Bioinformatics Analyst
> iPlant Collaborative
> BIO5 Institute, University of Arizona
> Phone: 520-977-5249
> Email: rogerab at email.arizona.edu
> Web: http://www.iplantcollaborative.org/
>             http://bio-it.arizona.edu/Roger_Barthelson_Home.html
>
>
>
>
>
>
> On 8/28/12 1:42 PM, "Cornel Ghiban" <ghiban at cshl.edu> wrote:
>
>> Hi,
>>
>> Is there an easy way of sending some data to the user?
>> What I'd like to do is send some BAM files into IGV.
>>
>> ( I've tried using a proxy web-script, but for some reason IGV fails to
>> load
>> the data. If I save the data to disk and then manually load it into IGV
>> it
>> works fine. )
>>
>> Thanks,
>> Cornel
>> _______________________________________________
>> Iplant-api-dev mailing list
>> Iplant-api-dev at iplantcollaborative.org
>> http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev
>