Hi, I' am trying to add built-in reference genomes for my local galaxy installation. I know this topic has been covered multiple times: I have looked through the discussion threads and the wiki (e.g. NGS Local Setup), but I' am still unsuccessful. Previously I have just loaded a reference genome through the history, but in the interest of saving time and space while I experiment with Galaxy I wish to use the built-in feature. Here is what I have tried: 1. Indexed ecoli.fa using bwa and put all files (fasta and index files) under /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ The directory looks like: -rwxrwxrwx@ 1 charlesmurphy staff 4706043 Mar 5 14:54 ecoli.fa -rwxrwxrwx 1 charlesmurphy staff 12 Mar 5 16:38 ecoli.fa.amb -rwxrwxrwx 1 charlesmurphy staff 111 Mar 5 16:38 ecoli.fa.ann -rwxrwxrwx 1 charlesmurphy staff 4639752 Mar 5 16:38 ecoli.fa.bwt -rwxrwxrwx 1 charlesmurphy staff 1159920 Mar 5 16:38 ecoli.fa.pac -rwxrwxrwx 1 charlesmurphy staff 2319888 Mar 5 16:38 ecoli.fa.sa 2. Downloaded and installed the bwa wrapper files from the Galaxy main toolshed, and put bwa in $PATH. 3. Added the following line to the bwa_index.loc (using tabs as the delimiter): ecoli ecoli ecoli /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa 4. Added the following line to builds.txt (using tabs as the delimiter): ecoli ecoli 5. Restarted Galaxy. The ecoli genome does not show up as a reference genome for BWA (Map with BWA for Illumina). Any help would be appreciated. Thanks, Charlie