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