Thanks a lot! It's really helpful!
I'm looking forward to seeing new version of galaxy / galaxy tool shed soon!
Dongjun
On 8/31/2011 2:38 PM, Greg Von Kuster wrote:
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 ___
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Greg Von Kuster
Galaxy Development Team
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