I just installed Galaxy in local Centos Vm.  I did my best to get everything 
working ( I think).  I followed the instructions in this Wiki 
(http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference 
genomes for the tools Bwa and Bowtie.  Here is what I did in details:

1.       I installed all the software and added them to the PATH and everything 
seems to be working.

2.       Then I created the indices as explained.

3.       I put all the indices in the same recommended directory structure and 
gave all access rights to the Galaxy user which runs the Galaxy server.

4.       I created the loc files (bowtie_indices.loc and 
bowtie_indices_color.loc and bwa_index.loc) and populate them with the 
recommended contents) and place them in ~/tool_data/ folder.

5.       I copied the xml and py files from this location and put them into 
https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping This 
step was not mentioned in the instruction but I thought this might be the cause.

6.       I restarted the server.

Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the reference 
genome in the list.  Can someone tell me what I missed or how to go about 
debugging it?

I appreciate any kind of help....

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