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"jen@bx.psu.edu To: "James Nelson"jcn@k-state.edu Cc: galaxy-user@bx.psu.edu 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.

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