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 <http://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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