-----Original Message-----
From: Hakeem Almabrazi 
Sent: Thursday, January 31, 2013 7:54 AM
To: 'Carlos Borroto'
Subject: RE: [galaxy-dev] install reference genome Bwa and Bowtie!

Thank you Carlos for your help,

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
#######################

The same issue is happening with bowtie.

Is there anything I need to do somewhere else in the system (DB, configuration 
files etc) i.e in ~ tool-data/shared/ucsc/builds.txt file.

Regards,
Hakeem


-----Original Message-----
From: Carlos Borroto [mailto:carlos.borr...@gmail.com] 
Sent: Wednesday, January 30, 2013 10:22 PM
To: Hakeem Almabrazi
Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie!

On Wed, Jan 30, 2013 at 7:19 PM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
> 4.       I created the loc files (bowtie_indices.loc and
> bowtie_indices_color.loc and bwa_index.loc) and populate them with the
> recommended contents) and place them in ~/tool_data/ folder.

Most of the time I run into this issue this is the step where I'm
messing up. Double check you are using TABs (not spaces) to separate
values in these files. Also check you have only one TAB between
values, some of the examples have more than one for pretty formatting
but that will cause the configuration not to work.

Hope it helps,
Carlos

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