Hi all,

I am a little confused as to the right way to configure my installed NGS tools.

>From the documentation I've found and from looking at the xml/python
wrappers, it looks to me like the NGS tool wrappers simply call the
tools and assume they will be in the galaxy account's PATH. For
instance, bwa_wrapper.py simply calls "bwa" in the shell. So it looks
to me like the default assumption is that bwa was installed as root
and is available to all users, and will always be on your PATH. Is
this right, or am I missing some configuration options that should
tell galaxy where to find the bwa binary?

If this is the case, what is the best way to install and maintain two
versions of the same tool? I can write code into the wrapper to find
the correct version of the tool in a given case, but I was wondering
if there is a more standard 'galaxy' way to configure this.

Sorry for the newbie questions again - I have been looking at the NGS
setup and Tools documentation, but I don't think I've found anything
on multiple installed versions of a tool. Also if there are any docs I
have missed on configuring path environment variables, please let me


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