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