Am Donnerstag, den 06.06.2013, 14:42 -0400 schrieb Sébastien Boisvert:
> On 06/06/13 02:32 PM, James Taylor wrote:
> >> I want to add Ray (a scalable de novo assembler for genomes and 
> >> metagenomes)
> >> to Galaxy.
> >
> > And I really want you to do this!
> 
> So we are at least two !

Joining the party! Make three out of it!

> >
> >> I will also have to write a wrapper for Ray to prepare the command line 
> >> from
> >> the options provided by the
> >> Galaxy API.
> >>
> >>
> >> But where is stored the executable (in my case, where is sdtored Ray) ?
> >>
> >> Does Galaxy include the specs to build all the tools available in
> >> Galaxy-Central ?
> >
> > No, we are gradually moving all the tools out of galaxy-central into
> > the Tool Shed. You probably want to look at this page:
> >
> >    
> > http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
> >
> > Which describes how you can add a recipe to the toolshed that will
> > install the Ray binaries.
> >
> 
> So Ray needs a C++ 1998 compiler and a MPI library (let's say g++ and 
> openmpi-bin). Are those already installed in Galaxy deployments ?

You can assume that gcc is installed. Nevertheless, openmpi-bin needs to
be installed. I would suggest to create a orphan-tool-dependency for
openmpi-bin.  For example have a look at:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53

And than make that orphan-tool-dep a requirement of your repository.

> Also, when is tool_dependencies.xml processed (I assume it is procesed when 
> re-loading the content of the shed into Galaxy ?

I don't understand the question, but if you install Ray the
tool_dependency file is read and at that time it will be installed and
the openmpi dependency.

Cheers,
Björn

> Thanks !
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