Update Pulsar on Test, resolve dependencies on Bridges using conda (a…

…fter modules) and run rnaSPAdes on Bridges
galaxyproject · Mar 27, 2017 · 7f263c2 · 7f263c2
1 parent 4324d0b
commit 7f263c2
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/files/galaxy/common/dynamic_rules/bridges_select.py b/files/galaxy/common/dynamic_rules/bridges_select.py
@@ -91,10 +91,10 @@ def dynamic_bridges_select( app, tool, job, user_email ):
                     mem = 960 * 1024 # 20 * 48 GB
                     walltime = '96:00:00'
 
-        elif tool_id == 'spades':
+        elif tool_id in ('spades', 'rnaspades'):
             # nothing to go off of yet so we'll just guess
-            mem = 240 * 1024
-            walltime = '24:00:00'
+            mem = 480 * 1024
+            walltime = '48:00:00'
 
         destination.params['submit_native_specification'] += ' --time=%s' % walltime
         destination.params['submit_native_specification'] += ' --mem=%s' % mem

diff --git a/files/pulsar/common/config/bridges_dependency_resolvers_conf.xml b/files/pulsar/common/config/bridges_dependency_resolvers_conf.xml
@@ -6,13 +6,14 @@
      package definitions, but by default look in the directory specified by tool_dependency_dir
      in Galaxy's config/galaxy.ini -->
   <galaxy_packages />
+  <modules modulecmd="/usr/bin/modulecmd" />
+  <conda auto_install="True" auto_init="True" />
+
   <galaxy_packages versionless="true" />
-  <conda />
+  <modules modulecmd="/usr/bin/modulecmd" versionless="true" default_indicator="default" />
   <conda versionless="true" />
 
 <!-- Example configuration of modules dependency resolver, uses Environment Modules -->
-  <modules modulecmd="/usr/bin/modulecmd" />
-  <modules modulecmd="/usr/bin/modulecmd" versionless="true" default_indicator="default" />
 <!--
 Attributes are:
 * modulecmd - path to modulecmd

diff --git a/stage/group_vars/pulsarservers.yml b/stage/group_vars/pulsarservers.yml
@@ -15,7 +15,7 @@ galaxy_instance_hostname: test.galaxyproject.org
 
 ## used by: galaxyprojectdotorg.pulsar
 pulsar_pip_install: true
-pulsar_changeset_id: 71b55968f4d162b9a0308fdf3837cb1d6031c8e9
+pulsar_changeset_id: 2a94561ccc33254ece49e83ab3d9c17bf88e5c35
 pulsar_venv_dir: "{{ pulsar_root }}/venv"
 pulsar_config_dir: "{{ pulsar_root }}/config"
 

diff --git a/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 b/templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
@@ -544,6 +544,7 @@
         <!-- bridges jobs -->
         <tool id="trinity_psc" destination="dynamic_bridges_select" handler="test_handler2" resources="bridges"/>
         <tool id="spades" destination="dynamic_bridges_select" handler="test_handler2" resources="bridges"/>
+        <tool id="rnaspades" destination="dynamic_bridges_select" handler="test_handler2" resources="bridges"/>
         <!-- trackster jobs -->
         <tool id="cufflinks" destination="slurm_multi_trackster">
             <param id="source">trackster</param>