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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