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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/

Reply via email to