Hi,
On 12/06/13 05:50 PM, Jennifer Jackson wrote:
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.
So if someone installs galaxy-dist, the person will have to pick up each tool
in the tool shed. Is that correct ?
Will the schema of XML files remain the same ?
Whether or not to have the repo binaries
self-install & config or not will be up to you.
You mean that some apps will self-install and other will require the
intervention of a system administrator.
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
You are right, I should have posted to -dev in the first place. Sorry.
So my deliverable to add Ray in galaxy is 2 XML files. Thanks.
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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