Hello Hakeem,

It is difficult to troubleshoot without knowing all the exact details of your configuration, but it sounds as if you are on the right path and the last few bits should be easy to reconcile with our documentation.

In particular, check that the builds.txt file contains the genomes that you are adding. Also, if you want to view or use our indexes (if we have them available for your genome), or just want to double check your indexes vs ours, the rsync service can be used. Both are described in this wiki:
http://wiki.galaxyproject.org/Admin/Data%20Integration

I am not sure that I understand step #5, but there is another confusing point here. You want the data and all tools under the primary Galaxy directory hierarchy or have the alternate locations specified in the universe config file. Also, it is important to not us symbolic paths in the .loc files - use the full hard path to the indexed data.

Hopefully this helps! If you do need more feedback, please be sure to leave the mailing list on the cc to help us track any reply,

Best,

Jen
Galaxy team

On 1/30/13 4:19 PM, Hakeem Almabrazi wrote:
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….



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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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