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

[Cornel Ghiban]

Hi Matt,

Thanks for letting us know about user "world" (I was sharing the files to a 
"dnasubway" user and then have this user stream the files directly to the 
browser).
But it still doesn't work since IGV insists on using the "range-byte" requests.

Thanks,
Cornel

On 8/28/2012 6:05 PM, Matthew Vaughn wrote:
> 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
>
>