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_too...
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 !