Toni,

As a quick work-around until set up natively, you may be able to use the Extract DNA tool with a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
See the example in: "Tools on the Main server", should work on any Galaxy set up as a production server

In short, you load a fasta version of the genome into your history and use it with tools. UCSC is the source for sacCer2, in the downloads area:
http://genome.ucsc.edu

Most, but not all, core tools from the Galaxy team have a custom genome support option on the form. When they don't, there is a reason (likely not practical from a indexing/memory usage perspective). Tools developed by the community set their own priority for this support.

Best,

Jen
Galaxy team

On 7/25/13 9:19 AM, Toni Delorey wrote:
Hello,

Thanks for your response. I can almost never get anything done on the public instance of Galaxy. It can take an entire day to even load a.bed file. When I was encountering the error I was on the Broad Instance.

Marco, I tried following the instructions above to ensure that genome was available but got lost. Is there a way to link this with the Broad Instance so I can use this tool?

Thanks,
Toni


On Tue, Jul 23, 2013 at 7:48 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Toni,

Bjoern is correct - if you are using a local Galaxy that does not have this reference genome available, it needs to be added. The "Extract DNA" tool requires a .2bit version of the genome available and the alignseq.loc file configured. More is here, section " LASTZ and EXTRACT Genomic DNA":
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

The builds.txt file would need to be intact and the genome assigned for this specific error to come up, but in general when adding new reference genomes, that file also needs to be adjusted. Instructions are on this wiki page, along with rsync instructions if you would like to get/model your data after ours:
http://wiki.galaxyproject.org/Admin/Data%20Integration

The public Main server and the cloud AMI both have this build available. So, if you are using the public server, and this error came up, the issue is likely related to a temporary, earlier issue with job dispatching. Processing load at this time is extremely high as this resolves - so a re-run may not be successful immediately, but do try again in a few hours or even tomorrow morning.

Our apologies for any confusion this may have caused,

Jen
Galaxy team


On 7/23/13 9:24 AM, Toni Delorey wrote:
Hello,

I'm trying to convert a .bed file to a FASTA file. I get the following error when I do.


"An error occurred with this dataset: No sequences are available for 'sacCer2', request them by reporting this error."

I'm not sure what the issue is?

Thanks,
Toni
--
Toni Marie Delorey
Regev Lab, 6175-OO
The Broad Institute of MIT and Harvard
7 Cambridge Center
Cambridge, MA 02141
Email: delorey@broadinstitute.org
Phone: 617-714-8225




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--
Toni Marie Delorey
Regev Lab, 6175-OO
The Broad Institute of MIT and Harvard
7 Cambridge Center
Cambridge, MA 02141
Email: delorey@broadinstitute.org
Phone: 617-714-8225



-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org