Hi Sébastien,

This all looks fine, except for the part about including this in the distribution. As James stated, we are moving to a model where eventually all tools will be sourced from the Tool Shed. That is where you should create your repository. Whether or not to have the repo binaries self-install & config or not will be up to you.


Going forward, you probably will want to start up a new thread for new questions and have discussions on the galaxy-...@bx.psu.edu mailing list. This will give your questions the most exposure to the development community.
http://wiki.galaxyproject.org/MailingLists#The_lists

Take care,

Jen
Galaxy team

On 6/12/13 8:05 AM, Sébastien Boisvert wrote:
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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___________________________________________________________
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/

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