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 _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/