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.cock@googlemail.com To: thisisjoel@hotmail.com CC: galaxy-dev@lists.bx.psu.edu
On Mon, Nov 5, 2012 at 5:34 PM, Joel Rosenberg <thisisjoel@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