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
ecoli   ecoli   ecoli
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.

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