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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