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:
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.
> Thanks !
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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