Hi John,

Thanks for your response. I had already installed that shed tool package
and I had added the datatype info to the datatypes_conf.xml file and I can
choose an sra datatype when I upload the file. I get this error after doing
those things. Perhaps I should contact Matthew Shirley and see if he can
help me out.

- Nik.

On Sun, Mar 29, 2015 at 5:50 PM, John Chilton <jmchil...@gmail.com> wrote:

> 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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>



-- 
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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