Remove embedded Pulsar from Main job config

galaxyproject · May 25, 2016 · 932903a · 932903a
1 parent 8f67686
commit 932903a
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Showing 2 changed files with 16 additions and 20 deletions.
diff --git a/files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml b/files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml
@@ -4,13 +4,13 @@
 
 ## Configure one or more named managers (more information on configuring managers
 ## can be found at http://pulsar.readthedocs.org/en/latest/job_managers.html).
-managers:
-  jetstream_iu:
-    type: queued_drmaa
-    staging_directory: /jetstream/iu-scratch0/main/jobs
-  #jetstream_tacc:
-  #  type: queued_drmaa
-  #  staging_directory: /jetstream/tacc-scratch0/main/jobs
+#managers:
+#  jetstream_iu:
+#    type: queued_drmaa
+#    staging_directory: /jetstream/iu-scratch0/main/jobs
+#  jetstream_tacc:
+#    type: queued_drmaa
+#    staging_directory: /jetstream/tacc-scratch0/main/jobs
 
 
 ## Mode to create job releated directories with. If unset

diff --git a/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 b/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2
@@ -14,9 +14,6 @@
             <param id="invalidjobexception_retries">5</param>
             <param id="internalexception_retries">5</param>
         </plugin>
-        <plugin id="embedded_pulsar_jetstream" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
-            <param id="pulsar_config">/srv/galaxy/main/config/pulsar_jetstream.yml</param>
-        </plugin>
         <plugin id="pulsar_jetstream" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"/>
         <plugin id="amqp_pulsar_stampede" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner">
             <param id="amqp_url">{{ galaxy_job_conf_amqp_url }}</param>
@@ -53,7 +50,6 @@
         <handler id="main_w1_handler2" tags="multi_handlers">
             <plugin id="local"/>
             <plugin id="slurm"/>
-            <plugin id="embedded_pulsar_jetstream"/>
             <plugin id="pulsar_jetstream"/>
             <plugin id="amqp_pulsar_stampede"/>
             <plugin id="amqp_pulsar_stampede_nagios"/>
@@ -70,7 +66,6 @@
         <handler id="main_w2_handler2" tags="multi_handlers">
             <plugin id="local"/>
             <plugin id="slurm"/>
-            <plugin id="embedded_pulsar_jetstream"/>
             <plugin id="pulsar_jetstream"/>
             <plugin id="amqp_pulsar_stampede"/>
             <plugin id="amqp_pulsar_stampede_nagios"/>
@@ -247,16 +242,17 @@
             <!-- this destination exists for the dynamic runner to read the native spec for testing -->
             <param id="nativeSpecification">--time=36:00:00 --nodes=1 --partition=multi</param>
         </destination>
-        <destination id="jetstream_iu_multi" runner="embedded_pulsar_jetstream" tags="jetstream">
-            <param id="manager">jetstream_iu</param>
-            <param id="submit_native_specification">--clusters=jetstream-iu --time=36:00:00 --nodes=1 --partition=multi</param>
+        <destination id="jetstream_iu_multi" runner="pulsar_jetstream" tags="jetstream">
+            <param id="url">http://jetstream-iu0.galaxyproject.org:8914/managers/jetstream</param>
+            <param id="transport">curl</param>
+            <param id="default_file_action">remote_transfer</param>
+            <param id="dependency_resolution">remote</param>
+            <param id="jobs_directory">/jetstream/scratch0/{{ galaxy_instance_codename }}/jobs</param>
+            <param id="submit_native_specification">--time=48:00:00 --nodes=1 --partition=multi</param>
             <param id="use_remote_datatypes">true</param>
             <param id="remote_metadata">true</param>
-            <!-- not working currently, see https://github.com/galaxyproject/pulsar/issues/110
-                 temporarily fixed with a copy at /cvmfs/main.galaxyproject.org/galaxy/datatypes_conf.xml
-            <param id="remote_property_galaxy_datatypes_config_file">/cvmfs/main.galaxyproject.org/galaxy/config/datatypes_conf.xml.sample</param>
-            -->
-            <param id="remote_property_galaxy_home">/cvmfs/main.galaxyproject.org/galaxy</param>
+            <param id="remote_property_galaxy_home">/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy</param>
+            <param id="remote_property_galaxy_datatypes_config_file">/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/config/datatypes_conf.xml</param>
             <param id="file_action_config">{{ galaxy_config_dir }}/pulsar_jetstream_actions.yml</param>
             <env file="/cvmfs/main.galaxyproject.org/venv/bin/activate" />
             <env id="LC_ALL">C</env>