Main: virtualenv and module fixes for Stampede

galaxyproject · Oct 9, 2015 · ad96740 · ad96740
1 parent 6757018
commit ad96740
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 b/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
@@ -155,6 +155,8 @@
             <param id="submit_native_specification">--time=48:00:00 --nodes=1 --ntasks=16 --partition=normal --account=TG-MCB140147</param>
             <param id="file_action_config">{{ galaxy_config_dir }}/pulsar_stampede_actions.yml</param>
             <param id="submit_user_email">$__user_email__</param>
+            <env exec="eval `/opt/apps/lmod/lmod/libexec/lmod bash purge`" />
+            <env file="/work/galaxy/main/galaxy/venv/bin/activate" />
         </destination>
         <destination id="pulsar_stampede_development" runner="amqp_pulsar_stampede">
             <param id="transport">curl</param>
@@ -170,6 +172,8 @@
             <param id="submit_native_specification">--time=00:30:00 --nodes=1 --ntasks=16 --partition=development --account=TG-MCB140147</param>
             <param id="file_action_config">{{ galaxy_config_dir }}/pulsar_stampede_actions.yml</param>
             <param id="submit_user_email">$__user_email__</param>
+            <env exec="eval `/opt/apps/lmod/lmod/libexec/lmod bash purge`" />
+            <env file="/work/galaxy/main/galaxy/venv/bin/activate" />
         </destination>
         <destination id="pulsar_stampede_nagios" runner="amqp_pulsar_stampede_nagios">
             <param id="transport">curl</param>
@@ -182,6 +186,8 @@
             <param id="remote_property_galaxy_config_file">/work/galaxy/main/galaxy/config/galaxy.ini</param>
             <param id="remote_property_galaxy_datatypes_config_file">/work/galaxy/main/galaxy/config/datatypes_conf.xml</param>
             <param id="file_action_config">{{ galaxy_config_dir }}/pulsar_stampede_actions.yml</param>
+            <env exec="eval `/opt/apps/lmod/lmod/libexec/lmod bash purge`" />
+            <env file="/work/galaxy/main/galaxy/venv/bin/activate" />
         </destination>
 
         <!-- local destination for nagios handler checks -->