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!
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...
From what I understand, I need to write 2 XML files in order to allow people to add Ray to their Galaxy instances: * ray.xml * tool_dependencies.xml These two files are self-contained -- that is Galaxy will install everything using tool_dependencies.xml (in my case, Open-MPI and Ray will be installed from source using the GNU compiler). Can I put these files directly in galaxy-dist/tools/sr_assembly/ray/ ? I suppose these 2 XML files will be distributed in galaxy-dist, but like Velvet, Ray won't be enabled by default in tool_conf.xml as assembly is more costly than mapping. Then, I need to add this to galaxy-dist/tool_conf.xml: <section name="NGS: Assembly" id="ngs_assembly"> <label text="Ray" id="ray"/> <tool file="sr_assembly/ray/ray.xml" /> </section> And finally, I just need to restart Galaxy. Is that correct ?
Which describes how you can add a recipe to the toolshed that will install the Ray binaries.