Hi,

The bowtie issue was resolved.  I resolved it by adding a table entry in the 
xml file "tool_data_table_conf.xml".  Hummmm :)  

....

Now, I am having the same issue with the SamTools displaying a reference 
genome....  :)...

My reference fasta file is located at (/usr/local/galaxy_data/hg19/samtools/)

I ran the following command to build the samtools index file
>samtools faidx hg19.fasta
This generated the hg19.fasta.fai

Here is the content of the above path after running the samtools indexing 
command:  

-rwxr-xr-x 1 galaxy galaxy hg19.fasta
-rw-rw-r-- 1 galaxy galaxy hg19.fasta.fai


For my sam_fa_indices.loc file here is the info I am using to reference the 
index file:
############
Index<TAB>hg19<TAB>/usr/local/galaxy_data/hg19/samtools/hg19.fasta
###########

I restarted my server but I do not see anything when I go to 
GUI->NGS:SamTools->Sam-To-Bam->Choose the source for the reference 
list:<HISTORY>

I do not see anything so far.

Is there something I am missing or is there anything else I need to change at 
this point.

Regards,



-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Thursday, January 31, 2013 10:50 AM
To: Carlos Borroto
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie!

Hi Carlos,

What about the bowtie?  I am still having the same issue with it.

Loc file: ~/tool-data/bowtie_indices.loc
Contents:
hg19    hg19    hg19    /usr/local/galaxy_data/hg19/bowtie/base/hg19 (WITH TABS)

listing all the files in (/usr/local/galaxy_data/hg19/bowtie/base/hg19)

-rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.1.ebwt
-rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.2.ebwt
-rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.3.ebwt
-rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.4.ebwt
-rw-rw-r-- 1 galaxy galaxy 37 
/usr/local/galaxy_data/hg19/bowtie/base/hg19.rev.1.ebw
-rw-rw-r-- 1 galaxy galaxy 
/usr/local/galaxy_data/hg19/bowtie/base/hg19.rev.2.ebw

Is there anything not right here?

I really appreciate your help...

...

-----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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