Further added support for pre-configured pbs/torque clusters

ARTbio · Nov 16, 2015 · 8c7573d · 8c7573d
1 parent dc137f0
commit 8c7573d
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Showing 5 changed files with 60 additions and 14 deletions.
diff --git a/defaults/main.yml b/defaults/main.yml
@@ -4,6 +4,8 @@
 galaxy_extras_config_nginx: true
 galaxy_extras_config_proftpd: true
 galaxy_extras_config_slurm: true
+galaxy_extras_config_pbs: false
+pbs_server_name: pbsqueue
 galaxy_extras_config_supervisor: true
 galaxy_extras_config_galaxy_root: true
 galaxy_extras_config_galaxy_job_metrics: true

diff --git a/local.yml b/local.yml
@@ -9,6 +9,8 @@
   tasks:
   - include: tasks/slurm.yml
     tags: slurm
+  - include: tasks/pbs.yml
+    tags: pbs
   - include: tasks/nginx.yml
     tags: nginx
   - include: tasks/proftpd.yml

diff --git a/tasks/main.yml b/tasks/main.yml
@@ -17,6 +17,9 @@
 - include: slurm.yml
   when: galaxy_extras_config_slurm
 
+- include: pbs.yml
+  when: galaxy_extras_config_pbs
+
 - include: supervisor.yml
   when: galaxy_extras_config_supervisor
 

diff --git a/tasks/pbs.yml b/tasks/pbs.yml
@@ -0,0 +1,22 @@
+- name: Install pip
+  apt: pkg={{ item }} state={{ galaxy_extras_apt_package_state }}
+  with_items:
+    - python-pip
+  when: galaxy_extras_install_packages
+
+- name: Install PBS/torque system packages
+  apt: pkg={{ item }} state={{ galaxy_extras_apt_package_state }}
+  with_items:
+    - torque-client
+    - pbs-drmaa-dev
+    - python-psutil
+  when: galaxy_extras_install_packages
+
+- name: "Fetch DRMAA egg for Galaxy"
+  shell: "{{ galaxy_venv_dir }}/bin/python {{ galaxy_root }}/scripts/fetch_eggs.py -e drmaa -c {{ galaxy_config_file }}"
+
+- name: "Install Galaxy job conf"
+  template: src=job_conf.xml.j2 dest={{galaxy_job_conf_path}}
+
+- name: "Set PBS/torque server name"
+  shell: "echo {{ pbs_server_name }} >> /etc/torque/server_name"
diff --git a/templates/job_conf.xml.j2 b/templates/job_conf.xml.j2
@@ -1,36 +1,53 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins workers="2">
+{% if galaxy_extras_config_slurm == True %}
         <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
             <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
         </plugin>
+{% endif %}
+{% if galaxy_extras_config_pbs == True %}
+        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner">
+          <param id="drmaa_library_path">/usr/lib/pbs-drmaa/lib/libdrmaa.so.1</param>
+        </plugin>
+{% endif %}
     </plugins>
     <handlers default="handlers">
 {% if galaxy_handler_processes == 0 %}
         <handler id="web0" tags="handlers"/>
 {% else %}
-{% for i in range(galaxy_handler_processes) %}
+  {% for i in range(galaxy_handler_processes) %}
         <handler id="handler{{ i }}" tags="handlers"/>
-{% endfor %}
+  {% endfor %}
 {% endif %}
     </handlers>
     <destinations default="cluster">
+{% if galaxy_extras_config_slurm == True %}
         <destination id="cluster" runner="slurm">
-{% if galaxy_source_shellrc %}
-            <env file="{{ galaxy_user_shellrc }}" />
+  {% if galaxy_source_shellrc %}
+          <env file="{{ galaxy_user_shellrc }}" />
+  {% endif %}
+          <param id="docker_enabled" from_environ="GALAXY_DOCKER_ENABLED">{{ galaxy_docker_enabled }}</param>
+          <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">{{ galaxy_docker_sudo }}</param>
+          <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
+          <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM">{{ galaxy_docker_volumes_from }}</param>
+          <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
+          <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">{{ galaxy_docker_volumes }}</param>
+        </destination>
 {% endif %}
-            <param id="docker_enabled" from_environ="GALAXY_DOCKER_ENABLED">{{ galaxy_docker_enabled }}</param>
-            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">{{ galaxy_docker_sudo }}</param>
-            <!-- The empty volumes from shouldn't affect
-                 Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use.
-            -->
-            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM">{{ galaxy_docker_volumes_from }}</param>
-          <!-- For a stock Galaxy instance and traditional job runner $defaults will
-               expand out as:
-               $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw
-          -->
+{% if galaxy_extras_config_pbs == True %}
+        <destination id="cluster" runner="pbs">
+  {% if galaxy_source_shellrc %}
+          <env file="{{ galaxy_user_shellrc }}" />
+  {% endif %}
+          <param id="docker_enabled" from_environ="GALAXY_DOCKER_ENABLED">{{ galaxy_docker_enabled }}</param>
+          <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">{{ galaxy_docker_sudo }}</param>
+          <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
+          <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM">{{ galaxy_docker_volumes_from }}</param>
+          <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
           <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">{{ galaxy_docker_volumes }}</param>
         </destination>
+{% endif %}
     </destinations>
     <limits>
     </limits>