On 06/06/13 02:32 PM, James Taylor wrote:
I want to add Ray (a scalable de novo assembler for genomes and metagenomes)
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
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
No, we are gradually moving all the tools out of galaxy-central into
the Tool Shed. You probably want to look at this page:
From what I understand, I need to write 2 XML files in order to allow people to
add Ray to their Galaxy instances:
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
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" />
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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