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

[Matthew Vaughn]

This is very close, as it presents a publicly available HTTP link for the BAM file, but it doesn't support byte-range fetch.

# Update to your own path, credentials, etc

# Make the BAM and BAI file readable to user 'world'
curl -X POST -sku "vaughn" -d "username=world" -d "canRead=true" -d "canWrite:false"  https://foundation.iplantcollaborative.org/io-v1/io/share/vaughn/testbam/bwa_s_6_BC12_sorted.bam

curl -X POST -sku "vaughn" -d "username=world" -d "canRead=true" -d "canWrite:false"  https://foundation.iplantcollaborative.org/io-v1/io/share/vaughn/testbam/bwa_s_6_BC12_sorted.bam.bai

# Access un-authenticated via the /download endpoint
curl -X GET -sk https://foundation.iplantc.org/io-v1/io/download/vaughn/testbam/bwa_s_6_BC12_sorted.bam

On Aug 28, 2012, at 4:20 PM, Cornel Ghiban wrote:

> 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
>> 
> _______________________________________________
> Iplant-api-dev mailing list
> Iplant-api-dev at iplantcollaborative.org
> http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev

--
Matthew W. Vaughn, Ph.D.,
Manager, Life Sciences Computing Group
Texas Advanced Computing Center
Austin, TX
vaughn at tacc.utexas.edu | (949) 436-6642