Good question about licenses! Sorry for the delayed answer, we had a bit
of discussion to review the existing strategy.
The general guiding policy is that if a tool is not completely public,
then it will not be released to the main code base/servers.
That said, you are correct - if something can be worked out with tool
author, coordination for a fully integrated wrapper is possible. Same
would be true for remote use of a 3rd party web tool - coordination with
the authors/owner would be needed first (although this is not the ideal
solution for galaxy main).
Meanwhile, a great place to add wrappers/remote access tools that have
special licensing is the tool shed (http://community.g2.bx.psu.edu/
The user comments field (displayed as Description) is free-form text and
any credits/license pointers can be added there for now. We may add in a
special field for this info later on, but for immediate use this is a
visible key that will likely satisfy many licensing rules.
Thanks again for more great ideas!
On 10/14/10 5:56 AM, Peter wrote:
On Fri, Oct 1, 2010 at 10:43 PM,
> Hi Jen,
> I was hoping for someone to say "yes, we did that for our Galaxy,
> here is the wrapper code", but I'll settle for encouragement. ;)
> As you will have seen, I'm focusing on the NCBI BLAST+
> wrappers at the moment, but wrapping the command line
> versions of TMHMM v2.0 and SignalP v3.0 would probably
> be next on my list of things to do in Galaxy.
The TMHMM v2.0 and SignalP v3.0 tools are free to
download and use for academics, but commercial or
other users would need to negiotiate a license:
There is nothing to stop me writing and sharing wrappers
for the tools, and installing and using TMHMM v2.0 and
SignalP v3.0 on a local Galaxy server for academic use.
However, I guess their licence would prevent TMHMM
v2.0 and SignalP v3.0 being included in the "public"
Galaxy server? One option might be to ask CBS if
they would allow Penn State University to make these
tools available via their public Galaxy server.
Has this issue of "academic only" licences come up
before for Galaxy wrapped tools?
Alternatively I might be able to write wrappers for the
CBS hosted TMHMM and SignalP webservice which
appears to be free to use by anyone, but that seems
less robust and they may be unhappy with the likely