I got it! Stupid mistake of relying on the editor to add tabs to the 
> hg19    hg19    hg19    ~/ngs/refgenomes/hg19/bwa_indexed/hg19 
statement, while it was replacing each tab with 4 spaces. Now all is working 
fine!

> ------------------------------
> 
> Message: 13
> Date: Wed, 9 Jan 2013 14:31:52 -0500
> From: Jorge Sepulveda <jls2...@columbia.edu>
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Blank local reference - even after following NGS
>       installation instructions
> Message-ID: <8ab4a885-98c8-4d44-b51f-cfcd2bd56...@columbia.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> 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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