Dataset not appearing as available input to SAM analyses

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Dataset not appearing as available input to SAM analyses

James Nelson
Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown.

Thanks
Clare Nelson

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Re: Dataset not appearing as available input to SAM analyses

Jen Hillman-Jackson
Hello Clare,

Perhaps the loaded pileup datasets are not assigned to the "pileup"
datatype? Click on the pencil icon in the right upper corner of the
loaded pileup dataset, then use "Edit Attributes -> Change data type".

Hopefully this helps,

Best,

Jen
Galaxy team


On 10/29/11 4:10 PM, James Nelson wrote:

> Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown.
>
> Thanks
> Clare Nelson
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
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>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Dataset not appearing as available input to SAM analyses

Jen Hillman-Jackson
In reply to this post by James Nelson
Hi Clare,

Galaxy is fairly transparent, so this occurs sometimes and can mean that
either the server is very busy or there is another problem, perhaps with
the dataset.

Please note that mpileup is not supported yet, just pileup, although
this is on our short list of to-do upgrades. If you used mpileup, this
could very likely be the root cause of the tool error ("server error").
You can track the upgrade to mpileup through this ticket:
https://bitbucket.org/galaxy/galaxy-central/issue/524

To troubleshoot a pileup file:

1 - double check the format of your data again the specification as
outlined on the tool form for "NGS: SAM Tools -> Generate pileup from
BAM dataset".

2 - try running the file type assignment again the job again to double
check against a transient error.

If pileup was used and the cause of the error is still unclear, we take
a look we can provide feedback. Please share a link to your history
using "Options -> Share or Publish" from the top of the history panel,
generate a share link, then email that back to me directly. Please note
which dataset presents the problem and confirm that "samtools pileup"
was used.

Thanks!

Jen
Galaxy team

On 11/2/11 8:12 AM, James Nelson wrote:

> Thanks Jen, but the very first time I tried changing the type to "pileup", Galaxy came back with
>
> Server Error
> An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
>
> I somehow don't think the user's supposed to see the "error logs" or exception reports, so what next?
>
> Clare
>
> ----- Original Message -----
> From: "Jennifer Jackson"<[hidden email]>
> To: "James Nelson"<[hidden email]>
> Cc: [hidden email]
> Sent: Wednesday, November 2, 2011 8:11:09 AM
> Subject: Re: [galaxy-user] Dataset not appearing as available input to SAM analyses
>
> Hello Clare,
>
> Perhaps the loaded pileup datasets are not assigned to the "pileup"
> datatype? Click on the pencil icon in the right upper corner of the
> loaded pileup dataset, then use "Edit Attributes ->  Change data type".
>
> Hopefully this helps,
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 10/29/11 4:10 PM, James Nelson wrote:
>> Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown.
>>
>> Thanks
>> Clare Nelson
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>     http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>     http://lists.bx.psu.edu/
>

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org