> > 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 

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" 
  <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 

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?


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