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

[Rion Dooley]

One of the things I've been working on for a few unrelated uses cases is partial data queries via the IO service. Basically you would specify an offset and range that you want returned. It would still support both online and offline data movement the same as before. One thing that I haven't thought through enough is what the range and offset would refer to. Is it bytes, characters, blocks, etc? If the data could be transformed into hdf, this might be easier, but I don't think that's the norm. Do you have any ideas on how we might approach this generally?


--
Rion Dooley, PhD
Manager, Web and Cloud Services Group
Texas Advanced Computing Center
dooley at tacc.utexas.edu | (512) 232 - 5043

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________________________________________
From: iplant-api-dev-bounces at iplantcollaborative.org [iplant-api-dev-bounces at iplantcollaborative.org] on behalf of Cornel Ghiban [ghiban at cshl.edu]
Sent: Tuesday, August 28, 2012 4:20 PM
To: Barthelson, Roger A - (rogerab)
Cc: iplant-api-dev at iplantcollaborative.org
Subject: Re: [Iplant-api-dev] loading iRODS data into the browser

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
>
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