On 14/02/11 17:45, Peter Cock wrote:
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.

Peter

Indeed, this workaround works! Thank you.
I added these lines to the beginning of my run.sh:
    PATH="/opt/local/bin:/opt/local/sbin:$PATH"
    export $PATH

Now, Galaxy can find Grinder, Velvet, etc....

Could Galaxy detect and use ~/.profile automatically if it exists? Alternatively, maybe there should be a place in the configuration file universe_wsgi.ini to specify which file to read environment variables from? Is it worth filing an enhancement request in the bug tracker?

Again, thanks for the help.

Florent




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