Hi Jianpeng,

For reference, this is the wiki with instructions:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

The first thing to double check is that the server has been restarted. This is necessary after adding new indexes.

The next check is to walk through the setup steps again and make sure that the data organization is correct (directory structure), the indexing is valid (can you run Bowtie on the command line with a small sample using this hg19 index?), and the loc files have the correct content. Even minor differences in loc file data rows, such as a space instead of a tab (or the reverse), can prevent an index from appearing in the drop-down menu for a tool.

After troubleshooting, please let us know if you continue to have problems. Let's keep the thread on the galaxy-...@bx.psu.edu mailing list (instead of using the galaxy-dev-ow...@lists.bx.psu.edu email, which is intended for resolving subscription problems). If we do need to share private data at some point, we can move to the galaxy-team-only galaxy-b...@bx.psu.edu list.

Thanks!

Jen
Galaxy team

On 3/22/12 1:29 PM, Xu, Jianpeng wrote:
Hi ,

I have installed a local galaxy on our own server. And I have installed
the hg18 built-in index reference genome for bowtie, and it shows up in
the list. Then I installed the hg19 built-in index using the same
method. But the hg19 is not listed on the bowtie. Can you tell me why
the hg19 does not show up? We use the exact same method to do hg18 and
hg19. It seems that hg18 works fine, but hg19 does not work.

Can you tell me how to fix it ?

Thanks,

Jianpeng


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