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 najoshi@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 najoshi@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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Very sorry I missed that part of your problem description. I will try to find some time to test this out also.

-John

On Tue, Mar 31, 2015 at 2:10 AM, Nikhil Joshi najoshi@ucdavis.edu wrote:

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 jmchilton@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 najoshi@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 najoshi@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)

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)