Binary datatypes like SRA need to be registered with Galaxy and have a
corresponding datatype definition class - out of the box no such
datatype is defined for SRA. Requiring this definition makes it a
little bit harder to for instance host malware on usegalaxy.org. Main
has a data source tool for fetching fastq files from EBI -

https://usegalaxy.org/tool_runner/data_source_redirect?tool_id=ebi_sra_main

To actually enable use of real SRA files locally - Matthew Shirley has
a nice tool shed package that should install the SRA toolkit and a
corresponding SRA datatypes that I would assume would allow SRA files
to be uploaded.

Hope this helps,
-John


On Tue, Mar 24, 2015 at 3:20 AM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
> It looks like it doesn't work in galaxy main either.
>
> On Fri, Mar 20, 2015 at 3:42 PM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
>>
>> Hi all,
>>
>> So it is time again for our next bioinformatics course using galaxy and I
>> am trying to add some new tools to our custom galaxy running in the Amazon
>> Cloud. I've installed the ncbi sra toolkit interface from the toolshed and
>> the sra toolkit is installed on our AMI. However, when I upload an SRA file
>> into our galaxy, the file is empty and I get this error:
>>
>> The uploaded binary file contains inappropriate content
>>
>> I am able to extract the fastq from the archive just fine on the command
>> line, so I know it's not a problem with the file itself. Is there a solution
>> to this?
>>
>> - Nik.
>>
>> --
>> Nikhil Joshi
>> Bioinformatics Analyst/Programmer
>> UC Davis Bioinformatics Core
>> http://bioinformatics.ucdavis.edu/
>> najoshi -at- ucdavis -dot- edu
>> 530.752.2698 (w)
>
>
>
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
>
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