Hi Hakeem,

The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We want this to be correct.

For the SAM->BAM tool - in the UI, there will never be a list of genomes - that is not one of the form options. This tool either interprets the database assigned to the input dataset (option "Choose the source for the reference list: Locally cashed") or allows the user to select a genome custom reference genome (option same, but "History").

So, to give this a test, run a dataset through it that has hg19 assigned as the reference and examine the results.

If you are curious about custom genomes, which are used as fasta file datasets from a user's history with tools (instead of installed reference genomes), more is here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Take care,

Jen
Galaxy team


On 2/1/13 6:40 AM, Hakeem Almabrazi wrote:
Thank you Jennifer for your help.

I already resolved the issues with Bwa and Bowtie.  I was misled with some 
missing instructions but I managed to resolved them by searching online.  Now I 
am stuck at the SAM Tools.... displaying a reference genome....  :)...  I will 
give more details at what I am doing hopefully someone can help.

My reference fasta (hg10.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 ~tool-data/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>

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

Regards,

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, January 31, 2013 6:45 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hello Hakeem,

It is difficult to troubleshoot without knowing all the exact details of
your configuration, but it sounds as if you are on the right path and
the last few bits should be easy to reconcile with our documentation.

In particular, check that the builds.txt file contains the genomes that
you are adding. Also, if you want to view or use our indexes (if we have
them available for your genome), or just want to double check your
indexes vs ours, the rsync service can be used. Both are described in
this wiki:
http://wiki.galaxyproject.org/Admin/Data%20Integration

I am not sure that I understand step #5, but there is another confusing
point here. You want the data and all tools under the primary Galaxy
directory hierarchy or have the alternate locations specified in the
universe config file. Also, it is important to not us symbolic paths in
the .loc files - use the full hard path to the indexed data.

Hopefully this helps! If you do need more feedback, please be sure to
leave the mailing list on the cc to help us track any reply,

Best,

Jen
Galaxy team

On 1/30/13 4:19 PM, Hakeem Almabrazi wrote:
Hi,

I just installed Galaxy in local Centos Vm.  I did my best to get
everything working ( I think).  I followed the instructions in this Wiki
(http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install
reference genomes for the tools Bwa and Bowtie.  Here is what I did in
details:

1.I installed all the software and added them to the PATH and everything
seems to be working.

2.Then I created the indices as explained.

3.I put all the indices in the same recommended directory structure and
gave all access rights to the Galaxy user which runs the Galaxy server.

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.

5.I copied the xml and py files from this location and put them into
~/tools/sr_mapping/....
https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping
This step was not mentioned in the instruction but I thought this might
be the cause.

6.I restarted the server.

Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the
reference genome in the list.  Can someone tell me what I missed or how
to go about debugging it?

I appreciate any kind of help....



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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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