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 lost.
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? -Joel ---------------------------------------- > Date: Mon, 5 Nov 2012 17:44:49 +0000 > Subject: Re: [galaxy-dev] Where should I put a tool's required binaries? > From: p.j.a.c...@googlemail.com > To: thisisj...@hotmail.com > CC: galaxy-dev@lists.bx.psu.edu > > On Mon, Nov 5, 2012 at 5:34 PM, Joel Rosenberg <thisisj...@hotmail.com> 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/