Thank you Carlos again.
I was just looking at that and in fact I got it to work by following the sample
file. I was misled by the tutorial
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup in regard to create
this file.
*******************
Setting Up loc File
Get the index files to an accessible location
Create the file bwa_index.loc in the Galaxy tool-data directory
You can add the following header line if you want:
#buildname filepath
with a single tab separating the two
Then start adding the entries for each build
The file's path should include the first part of the index files' names
(the base)
So if they are named like reference_in.fasta.amb and are stored in
/path/to/base/indices, the entry should be:
reference_in /path/to/base/indices/reference_in.fasta
a tab separating the two
**********************
Now it is working but I am still not clear about the header line
#<unique_build_id> <dbkey> <display_name>. Which one of the identifier names
should match the actual reference_in name? Or it does not matter?
Thanks
-----Original Message-----
From: Carlos Borroto [mailto:carlos.borr...@gmail.com]
Sent: Thursday, January 31, 2013 8:50 AM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: FW: [galaxy-dev] install reference genome Bwa and Bowtie!
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
>
> I was sure that was not the case (all in tabs). Here is my bwa_indices.loc
> file look like
> #####################
> #bwaReference /usr/local/galaxy_data/hg19/bwa/
> hg19_reference_genome
> /usr/local/galaxy_data/hg19/bwa/hg19_reference_genome.fasta
> #######################
>
This doesn't seem right, please take a look to the sample .loc file:
http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/file/ffa8aaa14f7c/tool-data/bwa_index.loc.sample
You need something like:
#<unique_build_id> <dbkey> <display_name> <file_path>
hg19 hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
Best,
Carlos
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