I'm trying to add mm10 to a Galaxy instance built using Mercurial on May 31st (using Postgres). I've added the .fa file, prepared bwa, bowtie, samtool indexes, etc., edited all of the .loc files for individual tools and restarted the server daemon. mm10 appears in the list of genomes available for these tools but doesn't appear in the list of all genomes when I try uploading a file (Get Data/Upload File from your computer) OR when I try adding the file through the admin library interface (Administration/Data/Manage libraries/Add datasets). I tried editing ~/galaxy-dist/scripts/loc_files/create_all_fasta_loc.py to add a line for "mm10". restarting Galaxy but that genome still doesn't appear in the list.
Do I need to edit an entry in Postgres? When I restart Galaxy without the daemon mode (or tail the paster.log) I see that clicking on Get Data/Upload File is calling GET /tool_runner?tool_id=upload1 for the <my URL>/root/tool_menu. Am I supposed to upload new genomes through the Library? screencast.g2.bx.psu.edu is still down so I can't watch the video tutorials about configuring custom genomes. I'd appreciate any suggestions. Thanks in advance! Adios, Larry Larry Helseth, Ph.D. Center for Molecular Medicine NorthShore University HealthSystem Evanston, IL
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