Hi, Charles, builds.txt is what tells the Galaxy framework about available genomes. Various binary index files created from those genomes are separately managed for specific tools since some folks won't need some application specific sets of indexes for any given genome - so you need to edit a different file! The BWA for illumina tool for example gets BWA index files from tool-data/bwa_index.loc so that's where the reference to your ecoli.fa and related BWA index files needs to be added - the format is described in the comments you'll find when you edit that file. Tabs for delimiters again and another restart should fix your problem for that tool? On Wed, Mar 6, 2013 at 11:46 AM, Charles Murphy <murphy.charlesj@gmail.com>wrote:
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