I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them? David Hoover Helix Systems Staff http://helix.nih.gov
On Wed, Nov 03, 2010 at 05:19:03PM -0400, David Hoover wrote:
I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them?
I set ours directly in run.sh. Make sure you use 'export' so it alters subprocesses too. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu
Perfect. Thanks! On Nov 3, 2010, at 5:24 PM, Ry4an Brase wrote: On Wed, Nov 03, 2010 at 05:19:03PM -0400, David Hoover wrote:
I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them?
I set ours directly in run.sh. Make sure you use 'export' so it alters subprocesses too. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On Nov 3, 2010, at 17:24, Ry4an Brase <ry4an+galaxy@msi.umn.edu> wrote:
On Wed, Nov 03, 2010 at 05:19:03PM -0400, David Hoover wrote:
I'm trying to enable the EMBOSS tools, and Galaxy is complaining it can't find the executables. Our local installation of EMBOSS is in a non-standard location (/usr/local/emboss/bin). I tried setting the $PATH variable in ~/.bashrc_profile and ~/.profile, but this had no effect. Where can I add the path to the EMBOSS tools so that Galaxy can find them?
I set ours directly in run.sh. Make sure you use 'export' so it alters subprocesses too.
If using a cluster, however, it has to be set up in the user's shell startup files, or ~/.sge_request for SGE. --nate
-- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
participants (3)
-
David Hoover -
Nate Coraor -
Ry4an Brase