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_tool_dependency_installation_and_compilation_with_installed_repositories


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.


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