I am wondering the similar thing. If I understand Kevin's post correctly, I
think the question really is: if the automated tools build is
the requirement for creating the shed tool version specific env.sh
automatically during the shed tool installation.
Take BWA on the Tool Shed as an example, during the installation, BWA
binary was built on the fly and the path
But in some cases, the automated tools build is not desirable. On the
cluster that serves our Galaxy, we have had BWA compiled with the hardware
optimized compiler, and I simply want to put existing BWA path to the
env.sh without compiling another BWA that will not be used.
So it makes sense (at least to me) that the shed tool installation always
create the specific env.sh and provides the automated tools build as an
On Tue, Nov 13, 2012 at 8:21 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hi Kevin,
> I'm not clear why you want to create a "dummy" env.sh file, so I may not
> be able to answer your question. However, see the following tool shed wiki
> page in case you want to create an env.sh file that is sourced when the
> tool(s) included in the installed repository is executed in the Galaxy
> instance in case this is what you're looking for.
> Greg Von Kuster
> On Nov 12, 2012, at 1:51 AM, Kevin Y wrote:
> > Hi dev list,
> > What is the simplest xml I can put into a tool_dependencies.xml
> > for it to create a dummy env.sh in tool-dependency/tool/version/
> > ..../awef234243/env.sh
> > And will this be sourced each time. Or does the dependency need to be
> > some sort of "successfully install" status for it to be sourced?
> > Ideally I would be elegant if there is a way to create this env.sh
> > easily as it's the best way for a galaxy admin to manage the different
> > versions of dependencies.
> > Thanks,
> > Kevin.
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: