problem with uploading SRA file to our custom galaxy

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problem with uploading SRA file to our custom galaxy

Nikhil Joshi-2
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)

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Re: problem with uploading SRA file to our custom galaxy

Nikhil Joshi-2
It looks like it doesn't work in galaxy main either.

On Fri, Mar 20, 2015 at 3:42 PM, Nikhil Joshi <[hidden email]> 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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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/

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Re: problem with uploading SRA file to our custom galaxy

John Chilton-4
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 <[hidden email]> wrote:

> It looks like it doesn't work in galaxy main either.
>
> On Fri, Mar 20, 2015 at 3:42 PM, Nikhil Joshi <[hidden email]> 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/
___________________________________________________________
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/
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Re: problem with uploading SRA file to our custom galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> wrote:
> It looks like it doesn't work in galaxy main either.
>
> On Fri, Mar 20, 2015 at 3:42 PM, Nikhil Joshi <[hidden email]> 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
>> <a href="tel:530.752.2698" value="+15307522698">530.752.2698 (w)
>
>
>
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> <a href="tel:530.752.2698" value="+15307522698">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)

___________________________________________________________
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:
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Re: problem with uploading SRA file to our custom galaxy

John Chilton-4
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
>> > It looks like it doesn't work in galaxy main either.
>> >
>> > On Fri, Mar 20, 2015 at 3:42 PM, Nikhil Joshi <[hidden email]>
>> > 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)
___________________________________________________________
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/