I have put up an instance of galaxy on the cloud and as a simple test am trying to retrieve hg19 sequences corresponding to a bed file using the Extract Genomic DNA tool. hg19 is supposed to be a "loaded, system installed build" yet I get an error message stating that "No sequences are available for hg19". A similar thing occurred with an mm9 request. What is being done wrong? Tom
Thomas Randall, PhD Bioinformatics Scientist, Contractor Integrative Bioinformatics National Institute of Environmental Health Sciences P.O. Box 12233, Research Triangle Park, NC 27709 randallta2@niehs.nih.govmailto:randallta2@niehs.nih.gov 919-541-2271
Hi Tom,
The cloud image has the reference data for hg19 and mm9. However, it does not come with fully configured loc files for every tool that takes advantage of all that preloaded data. Try updating the loc file for the Extract Genomic DNA tool.
Dave C.
On Wed, May 23, 2012 at 11:07 AM, Randall, Thomas (NIH/NIEHS) [C] < thomas.randall@nih.gov> wrote:
I have put up an instance of galaxy on the cloud and as a simple test am trying to retrieve hg19 sequences corresponding to a bed file using the Extract Genomic DNA tool. hg19 is supposed to be a “loaded, system installed build” yet I get an error message stating that “No sequences are available for hg19”. A similar thing occurred with an mm9 request. What is being done wrong?****
Tom****
Thomas Randall, PhD****
Bioinformatics Scientist, Contractor****
Integrative Bioinformatics****
National Institute of Environmental Health Sciences****
P.O. Box 12233, Research Triangle Park, NC 27709****
randallta2@niehs.nih.gov****
919-541-2271****
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:
Hi Tom,
An update from the CloudMan developers: This will be fixed in the next release, which is imminent.
Thanks,
Dave C.
On Thu, May 24, 2012 at 11:04 AM, Dave Clements clements@galaxyproject.orgwrote:
Hi Tom,
The cloud image has the reference data for hg19 and mm9. However, it does not come with fully configured loc files for every tool that takes advantage of all that preloaded data. Try updating the loc file for the Extract Genomic DNA tool.
Dave C.
On Wed, May 23, 2012 at 11:07 AM, Randall, Thomas (NIH/NIEHS) [C] < thomas.randall@nih.gov> wrote:
I have put up an instance of galaxy on the cloud and as a simple test am trying to retrieve hg19 sequences corresponding to a bed file using the Extract Genomic DNA tool. hg19 is supposed to be a “loaded, system installed build” yet I get an error message stating that “No sequences are available for hg19”. A similar thing occurred with an mm9 request. What is being done wrong?****
Tom****
Thomas Randall, PhD****
Bioinformatics Scientist, Contractor****
Integrative Bioinformatics****
National Institute of Environmental Health Sciences****
P.O. Box 12233, Research Triangle Park, NC 27709****
randallta2@niehs.nih.gov****
919-541-2271****
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://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/
galaxy-user@lists.galaxyproject.org
-
Dave Clements -
Randall, Thomas (NIH/NIEHS) [C]