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> 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
> Phone: 617-714-8225
>
>
>
>
> ___________________________________________________________
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>
>
> --
> Jennifer Hillman-Jackson
> Galaxy Support and Traininghttp://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
Phone: 617-714-8225
___________________________________________________________
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:

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To search Galaxy mailing lists use the unified search at:

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