I know this has been addressed in various posts at different times. However after extensive review of these posts and the galaxy wiki and spending several hours on this I am still no closer to my goal. I'm running a local instance of galaxy.
I need a step-by-step instruction on how to obtain reference genomes for the various tool shed tools. As admin, I've been able to download through 'Manage local data (beta)' the hg19 reference genome, which did this:
python /home/gxfinal/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py "/home/gxfinal/galaxy/database/files/000/dataset_322.dat" --dbkey_description 'Human Feb. 2009 (GRCh37/hg19) (hg19)'
I believe this has to be indexed by the various tools before it will appear in tool drop down menus. If this need to be done on the command line, that's fine I can do that but I need to know where this needs to be done, and what files should be present for a reference genome to appear in tool options.
A feel a step-by-step detailed guide would be invaluable for other users with the same problems. I feel that given Galaxy's easy interface it should be simpler than I'm making it out to be.
Could someone please help? Or point me towards what I need.