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