Hello Mathew,

If you already have mapped your data, then you can just upload the BAM/SAM dataset(s), sort if necessary, leave the database unassigned, and run MACS. This workflow has an example of how to sort a BAM file and send to MACS - you don't have to use this exactly, in fact the settings (especially for MACS) are likely not appropriate. Just examine the general sort rules and use the parts of it that make sense for your purposes, and run the tools independently or modify to create your own workflow:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/w/sort-bam-for-peak-calling-macs-tool

If you want to convert SAM-to-BAM (not really necessary) or when starting with raw sequence data that needs to be mapped (or find that you want to map it again), then the reference custom genome should be loaded along with the sequence data. Again, leave the database unassigned for all. The general protocol is covered in #3 from the Using Galaxy paper (make adjustments for tag size, effective genome size, etc. as needed, using the MACS documentation linked from the tool's page as a guide):
http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

To prepare, load, troubleshoot, and use a custom reference genome with tools (such as mapping tools), please see this wiki and the links it points to.
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
In short, tool forms that have a custom genome option will ask "Choose the source for the reference list:" or similar - you will select "History" and then select the dataset where your custom reference genome has been uploaded in fasta format and assigned the datatype "fasta". It is very important that the chromosome/scaffold identifiers in the reference genome and those in any other files that refer to it are identical (in for example, a SAM or GTF dataset). This is where doing all of the analysis within Galaxy can be sometimes easier, since our tools maintain this internal data consistency.

This should help to get you started, but please let us know if you need more help as the analysis proceeds,

Best,

Jen
Galaxy team

On 9/10/12 9:59 AM, Mathew Bunj wrote:
> I have  a chipseq data which ha sbeen alined against bacterial genome. I
> am trying to figure out how I can use peak calling MACS in Galaxy main
> server. Do I need to use the bactaerial genome (in genome option of data
> uplaod) in uplaoding the data. Could some one diect me if I can add my
> own custom genome for MACS program with in Galaxy main.
> Thanks
>
>
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