Hello Dongjun, see my answers to your question inline.

On Aug 28, 2011, at 10:12 AM, Dongjun Chung wrote:

> Hi All,
> 
> I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great 
> work.
> 
> I have a question regarding contribution of software to galaxy. We developed 
> a ChIP-seq peak calling algorithm and software (R package) and hope to 
> contribute it to galaxy. I have read the wiki and prior mailing list about 
> the contribution system but it is still somewhat confusing to me.
> 
> 1. It seems that I can contribute our software to "tool shed" if I prepare 
> appropriate code & definition files. Then, users can download and use it with 
> their locally installed galaxy. However, these files committed to tool shed 
> will not appear in galaxy main or test servers. Am I correct?

Tools from the Galaxy tool shed may or may not be available in the Galaxy test 
/ main servers hosted at Penn State.  

> 
> 2. What is clear relationship between main/test servers & tool shed?

The Galaxy tool shed enables the Galaxy community to share tools.  These tools 
are generally used in local Galaxy installations, but not available on the Penn 
State instances.

> Can we contribute our software to main or test servers as well?

The tools available on the Penn State servers are generally developed by the 
Galaxy core development team, and are available in the Galaxy distribution.  If 
your tools complement the tools currently available in the distribution, the 
Galaxy core development team may agree to include them.  However, see my 
comments 2 answers below regarding upcoming enhancements to Galaxy and the tool 
shed.

> Or only galaxy core developers can add new tools to galaxy main or test 
> servers?

Yes.

> If so, which software is considered to be added to servers? Are they chosen 
> from tools contributed to tool shed?

Currently, tools available in the distribution and on the Penn State instances 
are generally developed by the core Galaxy development team.  However, upcoming 
enhancements to Galaxy and the Galaxy tool shed will enable automatic 
installation of tools from the tool shed into local Galaxy instances, 
eliminating the necessity to include tools in the distribution.  This 
automation will be available fairly soon.

> 
> 3. If our software is a R package, then users need to download and install it 
> first in their R system before they use our software within their galaxy 
> system even in the case they have appropriate definition files. Am I right? 
> Or is there any better solution for this?

If your tools require R, then those that use your tools will need to install R 
in the Galaxy environment path so the tools will be functional.  Tools that 
have dependencies like this should include a <requirements> tag set in the tool 
config.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirements.3E_tag_set

> 
> Thanks!
> 
> Best,
> Dongjun ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to