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.laza...@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.charl...@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.laza...@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.charl...@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
>>>>
>>>>
>>>>
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