reference genome

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reference genome

Changyu Fan
Dear Sir or Madam,

We have installed our local Galaxy server and everything looks fine.
But there are some issues with reference genome index.

The BWA and Mageblast is working.  Here is how bwa_index.loc looks like:
hg18full    hg18    Human (Homo sapiens): hg18 Full /u03/galaxy/galaxy_data/hg18/seq/hg18full.fa

But Bowtie2, Bowtie, Lastz do not work.  When we choose "use a built-in index",nothing is listed in "Select a reference genome:" option.
The bowtie2_indices.loc looks like
hg18    hg18    Human(hg18) /u03/galaxy/galaxy_data/hg18/hg18full/bowtie2_index/hg18full

Here is the directory of bowtie2_index.
-rw-rw-r-- 1 galaxy galaxy 964771848 Jan 28 13:41 hg18full.1.bt2
-rw-rw-r-- 1 galaxy galaxy 720355432 Jan 28 13:41 hg18full.2.bt2
-rw-rw-r-- 1 galaxy galaxy     77255 Jan 28 12:49 hg18full.3.bt2
-rw-rw-r-- 1 galaxy galaxy 720355424 Jan 28 12:49 hg18full.4.bt2
lrwxrwxrwx 1 galaxy galaxy        21 Jan 28 12:47 hg18full.fa -> ../../seq/hg18full.fa
-rw-rw-r-- 1 galaxy galaxy 964771848 Jan 28 14:38 hg18full.rev.1.bt2
-rw-rw-r-- 1 galaxy galaxy 720355432 Jan 28 14:38 hg18full.rev.2.bt2


We did double check that the tabs was not replaced by multiple spaces in the .loc files. And Galaxy server was restarted each time we changed .loc file.
However, There is still no reference is available through the NGS: mapping Bowtie2.
How should we debug this? We could not find any errors. Is there any log file we should look into? Anything we missed here?

Thanks a lot.

Changyu 

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