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 !
___________________________________________________________
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
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/

Reply via email to