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