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 <j...@bx.psu.edu <mailto:j...@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: delo...@broadinstitute.org <mailto:delo...@broadinstitute.org>
    Phone: 617-714-8225 <tel:617-714-8225>




    ___________________________________________________________
    The Galaxy User list should be used for the discussion of
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    atusegalaxy.org  <http://usegalaxy.org>.  Please keep all replies on the 
list by
    using "reply all" in your mail client.  For discussion of
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    use the Galaxy Development list:

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    To manage your subscriptions to this and other Galaxy lists,
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-- Jennifer Hillman-Jackson
    Galaxy Support and Training
    http://galaxyproject.org




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



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

___________________________________________________________
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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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/

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