Thanks for your response. I solved the issue. We all know the .loc files use the tab character as the delimiter. I knew I was supposed to use tab and have been double checking, but the problem arises when I enter tab while editing with the two IDEs I use (mvim and Xcode). Apparently, what mvim and Xcode enter when I press the tab character (at least while editing .loc files) is not recognized by Galaxy. When I press the tab character, 5 spaces is entered while using mvim and 3 while using Xcode; whereas I assume Galaxy is looking for \t. I can edit the files using plain old text editor and finally install built-in reference genomes. Charlie On Tue, Mar 5, 2013 at 8:27 PM, Ross <ross.lazarus@gmail.com> wrote:
No, you need to follow the documentation in the relevant sample loc file - not name individual index files.
(Your loc file had already been edited then. Be warned that if the bwa_index entry in tool_data_table.xml file has also been hacked to change the field definitions, all bets are off)
The bwa_index.loc created the first time a fresh Galaxy checkout is run is copied from tool-data/bwa_index.loc.sample - there you'll find the documentation, which suggests that
ecoli\tecoli\tecoliLongNameDescription\t/Users/charlesmurphy/Desktop/Research/data/genome/ecoli/bwa/ecoli.fa
should work after a restart and a fresh reload of the tool in your browser so the new data are loaded from the loc file - assuming the Galaxy user has permission to read those index files of course.
If not, it's time to read the suggestions in the wiki about providing more details when posting questions to the list! eg what Galaxy release (eg hg heads), OS, platform, python version etc....
On Wed, Mar 6, 2013 at 12:59 PM, Charles Murphy <murphy.charlesj@gmail.com
wrote:
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