Re: [galaxy-user] How do I add Ray to Galaxy Central in the tool shed ?

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Re: [galaxy-user] How do I add Ray to Galaxy Central in the tool shed ?

Sébastien Boisvert
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 [hidden email] 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.
>>>
>>
>> ___________________________________________________________
>> 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/
>

___________________________________________________________
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Re: [galaxy-user] How do I add Ray to Galaxy Central in the tool shed ?

Jennifer Jackson
Hi again,

On Jun 13, 2013, at 1:23 PM, Sébastien Boisvert <[hidden email]> wrote:

> 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 ?

Not all right now, just the ones not in the distribution that they want to use. These are mostly wrappers - 3rd party binaries are always distinct installs, sometimes automatic, as the wiki explains.

>
> Will the schema of XML files remain the same ?

The tool XML is unchanged. But, the section for the tool is included in the master tool config XML, upon install, if I am interpreting this correctly. Again, the Tool Shed wiki is one of the best documented parts of Galaxy and has the details per use-case. You'll want to follow those instructions and follow the News Briefs for updates.

>
>> 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.

Yes.

>
>>
>> Going forward, you probably will want to start up a new thread for new
>> questions and have discussions on the [hidden email] 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.
>

No problem! We are here to help. You'll  just find the development community even more helpful with local install and tool development feedback as you get more involved. That list gives your questions the best exposure to them. The Galaxy project is created from the inputs of many people - the core team and our community.

Best wishes for your project,

Jen

>
> 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.
>>>
>>> _______________________________________________________

--
Jennifer Hillman-Jackson
Galaxy Support & Training
http://galaxyproject.org
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org