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.
Thanks!
Best,
Dongjun
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Greg Von Kuster
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