> Setting the environment for each tool just prior to running the tool is 
> clearly better.
>
> What I'm doing currently is loading an environment module just before running 
> a tool in Galaxy.

On our HPC cluster, I have configured Galaxy to source the following
from our modules system:

1) Global file as defined in universe_wsgi.ini
    environment_setup_file=setup-modules-for-galaxy.sh

^^ This setups the module environment so commands like "module load "
work. It does something similar to:
     source /data/apps/modules/Modules/default/init/bash 2>&1 &> /dev/null

2) Configured tool_dependency_dir as described here:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
    tool_dependency_dir=tool_dependency

For each requirement as specified the xml, galaxy will automatically
look in tool_dependency/<name>/default/env.sh

Each dependancy's env.sh then use our favorite command:

   module load blah/version

Cumbersome? Yup! But I believe its a nice elegant way of getting thing
to work with no mucking around in the xml file.


> This will enable my native EMBOSS wrapper to run the defined version of the 
> (system-installed) EMBOSS suite.
>  However, it would only be worth me writing this extension if there's a 
> likelihood of getting it into Galaxy.  Is there?

I truly like the idea and think it would. However, stepping into the
Galaxy devs shoes, a solution like this might only be best for those
using modules (small subset of users). Hopefully others can give their
thoughts. The con I see in this is that Galaxy already has the env.sh
solution which in my setup described above, does support modules....

> In the meantime, there's work going on in Galaxy land to package every 
> application wanted in Galaxy,
> by writing install scripts, encapsulating environment variables in tool XML 
> files, etc.  (There is difficulty
> here in writing install scripts which work on every platform, which I have 
> commented on previously.)

I saw that post last week and while I like the idea, folks like me who
realllllly do care about the version of GCC we use (and compile our
own versions of gcc) will not use it. However, that is going off topic
now :-)

Will wait and see what others say...

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Thu, Sep 12, 2013 at 4:03 PM, Guest, Simon
<simon.gu...@agresearch.co.nz> wrote:
>> > Another vote for the excellent modules system from us at AgResearch
>>
>> Galaxy's dependency injection works in a similar way, without requiring
>> all the external dependencies. We don't need unload since we compose a
>> unique environment for every tool execution. This is much cleaner that
>> loading everything into the environment before running Galaxy, we want
>> tools to be executed with as clean an environment as possible.
>
> Setting the environment for each tool just prior to running the tool is 
> clearly better.
>
> What I'm doing currently is loading an environment module just before running 
> a tool in Galaxy.  So far, I have done this in the tool XML file by prefixing 
> the command with a module load command, e.g.
>
>   <command>. /etc/profile; module load EMBOSS/5.0.0; infoseq -sequence 
> [snipped] </command>
>
> The ugly ". /etc/profile" is needed for technical reasons.  I don't like 
> this, as it's a bit hacky, but what it achieves is useful and flexible.
>
> I envisage an extension to the tool XML syntax which would let me write it 
> like this, say:
>
>   <requirements><requirement type="module" 
> version="5.0.0">EMBOSS</requirement></requirements>
>   <command>infoseq -sequence [snipped] </command>
>
> This will enable my native EMBOSS wrapper to run the defined version of the 
> (system-installed) EMBOSS suite.  However, it would only be worth me writing 
> this extension if there's a likelihood of getting it into Galaxy.  Is there?
>
> Here's where I'm coming from.  I already have most of the applications I want 
> installed on my system.  I am working on updating the RPMs to support 
> side-by-side installs of multiple versions, with version selection by the 
> environment modules facility.  This is a small change (and improvement) on 
> what I have today.  It's a work in progress, but it's a manageable amount of 
> work.  It's looking likely that this multi-version packaging approach may be 
> adopted by an official CentOS Scientific Repo, and this could change the 
> landscape in terms of packaging of scientific applications for major Linux 
> distributions.  Who knows, that's all in the future.
>
> In the meantime, there's work going on in Galaxy land to package every 
> application wanted in Galaxy, by writing install scripts, encapsulating 
> environment variables in tool XML files, etc.  (There is difficulty here in 
> writing install scripts which work on every platform, which I have commented 
> on previously.)
>
> The big question is, will the Galaxy team accept contributions to Galaxy to 
> support different ways of solving this packaging problem?  In particular, 
> allowing for environment modules to be loaded as part of running a tool, and 
> having this functionality in the toolshed?
>
> cheers,
> Simon
>
>
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