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
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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
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
