Hi,

So I removed the edit I made to the builds.txt file. I' am not sure I completely understand how you think I should edit the tool-data/bwa_index.loc file. Previously it contained only the following line (tab delimited):

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa

When I open the Map with BWA for Illumina tool in Galaxy, there are no reference genomes to select from when I have "Use a built-in index" selected. 

I've previously examined the comments in the tool-data/bwa_index.loc file. I interpreted that I need one line in the tool-data/bwa_index.loc file for each "index set". Just to be clear, you aren't suggesting that I add five additional lines for the files with the .amb, .ann, .bwt, .pac, and .sa extensions? So my tool-data/bwa_index.loc file contains:

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.amb

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.ann

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.bwt

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.pac

ecoli   ecoli   ecoli   /Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa.sa

I tried that and it does not work. Your response is appreciated.

Charlie

On Tue, Mar 5, 2013 at 7:11 PM, Ross <ross.lazarus@gmail.com> wrote:

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