Hi,

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 ~/tools/sr_mapping/…. 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….