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.borroto@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 halmabrazi@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/t...
You need something like: #<unique_build_id> <dbkey> <display_name> <file_path> hg19 hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
Best, Carlos