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
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
I appreciate any kind of help....
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