On Mon, Feb 14, 2011 at 7:17 AM, Florent Angly <florent.an...@gmail.com> wrote:
> Hi Alex,
> Thanks for the pointers! The fact that Galaxy only reads /etc/profile and
> not the profile of the user that runs it, ~/.profile, entirely explains why
> it cannot find Grinder or Velvet:
> I run Galaxy on a Mac OS X and I have many programs installed from MacPorts.
> All these programs get installed under /opt/local/bin/, which is outside of
> the usual Mac paths (to avoid any conflict). So, every user on this Mac has
> to have /opt/local/bin added to its path in its ~/.profile to be able to use
> MacPorts program. I did this for my galaxy user, but if Galaxy does not read
> ~/.profile, then it won't find the programs I installed.
> I am surprised that you report that Galaxy does not read ~/.profile in fact,
> because on this wiki page,
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, it
> is advised to set up the $TEMP environment variable for Galaxy. How is one
> supposed to do that? I don't think that it would be advisable to ask people
> to edit their system-wide /etc/profile...
> So, how do I have to setup environment variables so that they will be used
> by Galaxy?

We do it in run.sh but this is partly because we're running Galaxy under
a non-login account, so there is no home directory.

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