Re: [galaxy-user] An idea for sharing tools
At the moment, the main repo is maintained by the galaxy team, and
that is fine and makes sense. However, I'm sure there is a lot of
duplicated work between the users when adding other tools in. For
example, there was a conversation the other day about adding in awk.
Someone had already done this, so the best idea would be if I could
pull in that definition and enable it with minimum effort. I have
already added tools (exonerate, restriction mapper, etc, etc) that may
be of use to other people. Not sure the best way to go about this,
but if my understanding of mercurial is right, we can simply offer
another repo for people to pull changes from.
This is something we're very interested in facilitating. For the long
term, we're hoping to provide a structured / wiki environment for
people to share tools and suites of tools, as well as providing more
support in the application for adding self-contained tool suites to a
Galaxy instance, injecting local configuration into tools and tool
suites, et cetera.
However, we'd also be very happy to see the mailing list used for this
at the moment, and might even be able to open up a section of the wiki
for users to list the tools they are making available.
Or perhaps there
is a better way (eg patches submitted to trac)? Another question is
what kind of tools would the core team accept for inclusion in the
main dist?
This is much trickier. We have to carefully consider two things when
including a tool in the "default" set.
1) Quality -- we want to integrate the best possible tools for
specific tasks, since one a tool starts being used, and has workflows
and histories that depend on it, it is difficult to change
substantially or replace. Sharing tools helps us here: if the user
community comes to a consensus that a tool is useful, that is a good
argument for including it upstream.
2) Security -- this is probably an even bigger concern. Tools like the
"awk" tool are pretty dangerous. Until / unless the Galaxy framework
can enforce complete tool isolation we definitely don't want to
include a tool like this in the main distribution.
-- jt
James Taylor
Assistant Professor
Department of Biology
Department of Mathematics & Computer Science
Emory University