[BioC] Editing AnnBuilder function "getSrcUrl"

[Seth Falcon]

Hi Dermot,

John Zhang <jzhang at jimmy.harvard.edu> writes:
>  
>>
>>I've been trying to use AnnBuilder (also Resourcerer|) to build
>>annotation package for Bos Taurus  and I know I need to edit "species"
>>in a number of functions (I expect) in order to do this. I have been
>>following discussion (links below) on this topic which indicate that I
>>need to edit the "getSrcUrl" function in AnnBuilder. However, I can't
>>find this function or "downloadSourceData.R " anywhere. Where is this
>>function and how can I edit it ? Thanks in advance.
>>
>
> getSrcUrl is in the file named getSrcUrl.R. It will be hard to get it to work by 
> editing functions within R as some of the functions are not included in the 
> NAMESPACE. You will have to get the source code and work from there. There are 
> several places you will need to change (basically by adding code to handle a new 
> organism)

To get the source code, you can either:

 1. Install Subversion (http://subversion.tigris.org/), get a working
    copy of the devel sources for AnnBuilder:

       svn co --username=readonly --password=readonly
       https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnBuilder

or

 2. Download the source package (.tar.gz) from here:
    http://bioconductor.org/packages/release/bioc/html/AnnBuilder.html

Learning svn may seem intimidating, but you can get started in small
steps.  Installing and doing a checkout to download a copy of the
source code is a good way to start.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org