Hello Celso,
This problem is occurring in a local install of Galaxy? If so, then you
will need to set up the reference genome to be used with tools.
Instructions to do so are on these wiki pages:
Basic instructions, you will need to move on to "Advanced Configuration":
http://wiki.galaxyproject.org/Admin/Get%20Galaxy
Tool set up (the header is most important for you now, since BWA is
already installed):
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
Data set up:
A version of your genome is available via rsync, with the dbkey
"Zea_mays_B73_RefGen_v2". Or, you can create your own indexes. The
"builds.txt" list is not optional, so make sure not to skip that part
and to restart your server after all steps in the set-up are complete.
http://wiki.galaxyproject.org/Admin/Data%20Integration
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Next time, please send questions directly to the mailing list. This will
get you the speediest reply.
Take care,
Jen
Galaxy team
On 4/8/13 12:11 PM, c cortes wrote:
Hello Jen, my name is Celso, i'm trying to map some reads from maize
to the reference genome B73 in Galaxy. However when i try with map
with BWA for Illumina in the option "select a reference genome" none
file appears neither for "use a built-in index" nor "use one from the
history options". I downloaded the B73 file as a fasta file, but my
doubt is the way of upload my reference genome in orden to it apperas
in Galaxy for mapping
Kind regards
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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