Hi,

I set up a local galaxy in my MacPro on 1/3/2013 using:
hg clone https://bitbucket.org/galaxy/galaxy-dist/

into this directory:
~/ngs/applications/galaxy-dist

Indexed hg19.fa using bwa index to ~/ngs/refgenomes/hg19/bwa_indexed/
        -rw-r--r--    1      JS    staff  6597              Jan      2      
15:03      hg19.fa.amb
        -rw-r--r--    1      JS    staff  6844              Jan      2      
15:03      hg19.fa.ann
        -rw-r--r--    1      JS    staff  3101804844  Jan      2      15:02     
 hg19.fa.bwt
        -rw-r--r--    1      JS    staff  775451186    Jan      2      15:03    
  hg19.fa.pac
        -rw-r--r--    1      JS    staff  1550902424  Jan      2      15:06     
 hg19.fa.sa

Added:
hg19    hg19    hg19    ~/ngs/refgenomes/hg19/bwa_indexed/hg19 
to this file:
 
~/ngs/applications/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/tool-data/bwa_index.loc

BWA shows up on the galaxy tools list, but the local reference genome box 
remains empty. It runs fine when I use a reference sequence (chr22.fa) from 
history.

If I download bwa (or bowtie2) and install according to the steps in 
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I have the same problem 
(empty local reference).

What am I missing?

Jorge Sepulveda, MD, PhD
Associate Director for Laboratory Medicine,
Medical Director of Laboratory Informatics,
Columbia University Medical Center
Associate Professor,
Department of Pathology & Cell Biology
Columbia University College of Physicians and Surgeons
PH1590B
622 W 168 St
New York, NY 10032
Cell: (917) 862-6050
Office: 212-305-6360
E-mail:jls2...@columbia.edu


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