Thanks Peter,

I tried doing something similar, but there wasn't a location in the galaxy 
user's $PATH that would persist across a cluster reboot or could be snapshotted 
(like the tools or data volumes). Adding /mnt/galaxyTools/my_dep_binaries or 
something to the $PATH would work temporarily, but not past a reboot as 
/home/galaxy/.bashrc, /etc/environment, etc are part of the AMI and would be 

In your cluster, wouldn't the galaxy user's ${HOME}/bin be transient? Are you 
running with a different EC2 setup or using a different AMI?


> Date: Mon, 5 Nov 2012 17:44:49 +0000
> Subject: Re: [galaxy-dev] Where should I put a tool's required binaries?
> From:
> To:
> CC:
> On Mon, Nov 5, 2012 at 5:34 PM, Joel Rosenberg <> wrote:
> >
> > Sorry for bumping this, but it seems like such a standard boilerplate
> > step of installing a tool that someone muts know how.
> >
> > -Joel
> >
> Personally I've just been installing them on the $PATH, typically
> under $HOME/bin of the Galaxy user which is on our Galaxy
> user account's $PATH.
> Peter
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