Great - I have added the option to the pull request
https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/d72967b2b7b25ba02584880526c7b28cab6970e7
as well as an option to supply a command instead of a file so you can
specify the module load directly in job_conf.xml without having to
create a file. Barring objections, I will merge this pull request
later today or early next week and it should be available in the June
release.

All of that said - I agree with Bjoern approach completely and would
go one step further - if working with the packager to modify the tool
to add a package tag that you can create a standard env.sh file for
that would be the 'recommend' solution :).

-John

On Fri, Apr 25, 2014 at 9:06 AM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> Hi Ida,
>
> now I got it.
> I may have an idea, not tested, but you could try the following.
>
> - Add a file under $galaxy_tools/R_env/3.1.0/env.sh
> - Create a symlink from $galaxy_tools/R_env/default/ to
> $galaxy_tools/R_env/3.1.0/
> - change your requirement tag to
> <requirement type="package">R_env</requirement>
>
> Now you can put in everything you want have in the env.sh file. That file
> will be sourced as soon as your tool will be executed. For example you can
> load your module.
>
> Hope that works!
> Thanks,
> Bjoern
>
>
>> Dear  Björn,
>>
>> maybe I could change the tool, which is not mine, and which I don't want
>> to maintain to use a specific R-version that is already available on our
>> cluster and
>> which I can put into my path with "module load R/3.1.0-devel" (
>> http://modules.sourceforge.net/)
>>
>> there even is a requirements in the wrapper which is not fulfilled (these
>> versions are not available at the moment) and still it installed without
>> problems.
>>    <requirements>
>>      <requirement type="R-module" version="3.5.27">edgeR</requirement>
>>      <requirement type="R-module" version="3.18.13">limma</requirement>
>>    </requirements>
>>
>> This requirements tags looks also rather inflexible to me. With an
>> additional level of user configurable indirection it would be possible to
>> make the tools
>> fit to different infrastructures without having to use binaries provided
>> by somebody else, taking up space for just one tool etc...
>>
>> Currently for jobs that are not run locally there is a general
>> environment_setup_file. There could be one optional environment_setup_file
>> for every job (or destination).
>>
>> In the end I created yet another wrapper.
>>
>> best,
>> ido
>>
>>
>> On Apr 25, 2014, at 2:34 PM, Björn Grüning <bjoern.gruen...@gmail.com>
>> wrote:
>>
>>> Hi Ido,
>>>
>>> I do not get your question in all detail, but it is possible to define a
>>> tool_dependencies.xml with a specific R version, + R libraries and use only
>>> that specific version from your tool with <requirement> tags.
>>>
>>> For an example please see various R tools from:
>>>
>>> https://github.com/bgruening/galaxytools
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> Am 25.04.2014 14:25, schrieb Ido Tamir:
>>>>
>>>> Hi,
>>>> has anything changed in galaxy in this regard?
>>>> Any way to modify an environment before a tools is run?
>>>>
>>>> I now have a tool relying on R-devel and bioconductor devel, both of
>>>> which I can load in a module.
>>>> The tool comes from the toolshed with xml like:
>>>>
>>>> <command interpreter="Rscript">
>>>> …
>>>>
>>>>
>>>> I don't want to hack around in the tool itself, but simply load the
>>>> necessary R-version.
>>>>
>>>> thank you very much,
>>>> ido
>>>>
>>>>
>>>> On Sep 13, 2013, at 3:23 AM, "Guest, Simon"
>>>> <simon.gu...@agresearch.co.nz> wrote:
>>>>
>>>>> Just been reading a bit more about the Galaxy packaging system.  Here's
>>>>> a slight modification to what I was suggesting that might fit in a bit
>>>>> better.  Apologies for not being more familiar with the existing system
>>>>> before proposing extensions.
>>>>>
>>>>> Recall that my goal is to support using a system-installed (native)
>>>>> package, at a defined version, which I aim to achieve by loading the
>>>>> appropriate environment module before running a tool.
>>>>>
>>>>> We still have tool_dependencies.xml defining a package at a particular
>>>>> version, but rather than download and build the source code, there's just 
>>>>> a
>>>>> directive that says how to pick up the correct program version at runtime,
>>>>> e.g. which environment module to load.
>>>>>
>>>>> So instead of the tool_dependencies.xml fragment:
>>>>> <tool_dependency>
>>>>>     <package name="bwa" version="0.6.2">
>>>>>         <install version="1.0">
>>>>>             <actions>
>>>>>                 <action
>>>>> type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2</action>
>>>>>                 <action type="shell_command">make</action>
>>>>>                 <action type="move_file">
>>>>>                     <source>bwa</source>
>>>>>                     <destination>$INSTALL_DIR/bin</destination>
>>>>>                 </action>
>>>>>                 <action type="set_environment">
>>>>>                     <environment_variable name="PATH"
>>>>> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>>>>>                 </action>
>>>>>             </actions>
>>>>>         </install>
>>>>>     </package>
>>>>> </tool_dependency>
>>>>>
>>>>> We have something like this (NB: element and attribute names are for
>>>>> illustrative purposes only):
>>>>>
>>>>> <tool_dependency>
>>>>>     <package name="bwa" version="0.6.2">
>>>>>         <use_native>
>>>>>             <actions>
>>>>>                 <action type="module_load">bwa/0.6.2</action>
>>>>>             </actions>
>>>>>         </use_native>
>>>>>     </package>
>>>>> </tool_dependency>
>>>>>
>>>>> This causes the right thing (module load bwa/0.6.2) to be stuck into
>>>>> the dependencies env.sh file when this package is installed from the
>>>>> toolshed.  We could call this toolshed tool native_package_bwa_0_6_2, to
>>>>> avoid confusion with the existing download-and-make one.
>>>>>
>>>>> We might want a bit of flexibility on what actions are supported (in
>>>>> case we want to support Software Collections, for example).
>>>>>
>>>>> What do you think?
>>>>>
>>>>> cheers,
>>>>> Simon
>>>>>
>>>>> PS: In case it wasn't already clear, solving this problem well is quite
>>>>> important to us here at AgResearch.  ;-)
>>>>>
>>>>>
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>>>>
>>>>
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