Merge branch 'release/1.0.0'

roles/grid-engine/tasks/master.yml

@@ -9,6 +9,7 @@
 
 - name: SGE | Template act_qmaster
   template: src=act_qmaster.j2 dest=/var/lib/gridengine/default/common/act_qmaster
+  when: docker is not defined
 
 - name: SGE | Ensure gridengine-master started 
   service: name=gridengine-master state=started
@@ -17,14 +18,17 @@
   command: qconf -as {{ inventory_hostname }}
   register: configure_master_as
   changed_when: not 'already exists' in configure_master_as.stderr
+  when: docker is not defined
 
 - name: SGE | Make a directory for our SGE templates
   file: state=directory path=/etc/gridengine/templates mode=0744
+  when: docker is not defined
 
 # setup memory as a consumable resource
 - name: SGE | Template memory configuration file
   template: src=sc.j2 dest=/etc/gridengine/templates/sge_sc
   register: memory_template
+  when: docker is not defined
 
 - name: SGE | Setup memory as consumable resource
   command: qconf -Mc /etc/gridengine/templates/sge_sc
@@ -38,30 +42,31 @@
   shell: qconf -su users | grep -E "^entries" | cut -f2 -d " "
   register: sge_current_users
   changed_when: false
+  when: docker is not defined
 
 - name: SGE | Add the capsid user
   command: qconf -au capsid users
-  when: not 'capsid' in sge_current_users.stdout.split(',')
+  when: docker is not defined and not 'capsid' in sge_current_users.stdout.split(',') 
 
 # loop through and template worker hosts
 - name: SGE | Generate execution host templates
   template: src=execution_host.j2 dest=/etc/gridengine/templates/sge_execution_host_{{ item }}.sh mode=0555
-  when: not single_node
+  when: not single_node and docker is not defined
   with_items: groups.worker
   register: execution_host_template
 
 # loop through and setup worker hosts, if this was better it would modify existing hosts as well instead of ignoring errors
 - name: SGE | Add worker hosts as execution hosts
   shell: export EDITOR=/etc/gridengine/templates/sge_execution_host_{{ item }}.sh && qconf -ae ; qconf -me {{ item }}
   with_items: groups.worker
-  when: execution_host_template.changed 
+  when: execution_host_template.changed
   ignore_errors: yes
 
   # add the master as an execution host if we only have one node
 - name: SGE | Single node execution host templates
   template: src=execution_selfhost.j2 dest=/etc/gridengine/templates/sge_execution_host_master.sh mode=0555
   register: execution_host_template
-  when: single_node
+  when: single_node and docker is not defined
 
 - name: SGE | Single node host as execution host
   shell: export EDITOR=/etc/gridengine/templates/sge_execution_host_master.sh && qconf -ae ; qconf -me master
@@ -74,35 +79,39 @@
   ignore_errors: yes
   register: sge_current_host_groups
   changed_when: false
+  when: docker is not defined
 
 # The template now handles the hostlist properly
 - name: SGE | Template host group configuration
   template: src=ahgrp.j2 dest=/etc/gridengine/templates/sge_ahgrp
-  when: not '@allhosts' in sge_current_host_groups.stdout_lines
+  when: docker is not defined and not '@allhosts' in sge_current_host_groups.stdout_lines 
 
 - name: SGE | Add the host group configuration
   command: qconf -Ahgrp /etc/gridengine/templates/sge_ahgrp
-  when: not '@allhosts' in sge_current_host_groups.stdout_lines
+  when: docker is not defined and not '@allhosts' in sge_current_host_groups.stdout_lines
 
 # Again, we don't want to do this if it already exists
 - name: SGE | Check current queues
   command: qconf -sql
   ignore_errors: yes
   register: sge_current_queues
   changed_when: false
+  when: docker is not defined
 
 # template handles hostlist, worker queue slots, target load average
 - name: SGE | Template main queue
   template: src=aq.j2 dest=/etc/gridengine/templates/sge_aq
   register: main_queue_template
+  when: docker is not defined
 
 - name: SGE | Add main queue
   command: qconf -Aq /etc/gridengine/templates/sge_aq
-  when: not 'main.q' in sge_current_queues.stdout_lines
+  when: docker is not defined and not 'main.q' in sge_current_queues.stdout_lines
 
 - name: SGE | Template modify queue
   template: src=mq.j2 dest=/etc/gridengine/templates/sge_mq.sh mode=0555
   register: modify_main_queue_template
+  when: docker is not defined
 
 - name: SGE | Modify main queue
   shell: export EDITOR=/etc/gridengine/templates/sge_mq.sh && qconf -mq main.q 
@@ -111,20 +120,21 @@
 - name: SGE | Check parallel environment status
   command: qconf -sp serial
   ignore_errors: yes
-  when: grid_engine_master == True
+  when: grid_engine_master == True and docker is not defined
   register: sge_parallel_env
   changed_when: false  
 
 - name: SGE | Template serial parallel environment file
   template: src=serial_profile.j2 dest=/etc/gridengine/templates/sge_serial_profile
   register: serial_profile
+  when: docker is not defined
 
 # Again, if this was better, we would re-create the environment if there were changes in the template
 - name: SGE | Setup serial profile environment
   command: "{{ item }}"
   with_items:
       - qconf -Ap /etc/gridengine/templates/sge_serial_profile
       - qconf -aattr queue pe_list serial main.q
-  when:  "'serial is not a parallel environment' in sge_parallel_env.stderr or serial_profile.changed"
+  when:  "docker is not defined and 'serial is not a parallel environment' in sge_parallel_env.stderr or docker is not defined and serial_profile.changed"
 
 # TODO: bindle 1.2.1 re-runs the sge setup script on reboot. Determine whether this is really needed

roles/postgres/tasks/main.yml

@@ -12,11 +12,27 @@
     regexp="LC_ALL"
     line="LC_ALL=\"en_US.utf8\""
 
+# from https://github.com/zenoamaro/ansible-postgresql
+- name: Adding APT repository key
+  when: ansible_os_family == 'Debian'
+  sudo: yes
+  register: _repo_key
+  apt_key:
+    id: ACCC4CF8
+    url: https://www.postgresql.org/media/keys/ACCC4CF8.asc
+
+- name: Add PostgreSQL official APT repository
+  when: ansible_os_family == 'Debian'
+  sudo: yes
+  register: _repo
+  apt_repository:
+    repo: "deb http://apt.postgresql.org/pub/repos/apt/ {{ansible_distribution_release}}-pgdg main"
+
 - name: install postgres pkgs
   apt: pkg={{ item }} state=present update_cache=yes cache_valid_time=3600
   with_items:
     - libpq-dev
-    - postgresql
+    - postgresql-9.1
     - python-psycopg2
 
 - name: setup pg_hba file

roles/seqware-common-infrastructure/tasks/main.yml

@@ -76,10 +76,12 @@
 - name:  Set up Hadoop HDFS Local Storage
   file: path={{ item.path }} state={{ item.state }} owner={{ item.owner }} recurse={{ item.recurse }} mode={{ item.mode}}
   with_items:
+     - { state: 'directory', path: '/data', owner: 'hdfs', group: 'hdfs', recurse: 'yes', mode: '0777' }
+     - { state: 'directory', path: '/data/1', owner: 'hdfs', group: 'hdfs', recurse: 'yes', mode: '0777' }
      - { state: 'directory', path: '/data/1/dfs/nn', owner: 'hdfs', group: 'hdfs', recurse: 'yes', mode: '0700' }
      - { state: 'directory', path: '/data/1/dfs/dn', owner: 'hdfs', group: 'hdfs', recurse: 'yes', mode: '0700' }
-     - { state: 'directory', path: '/data/1/mapred', owner: 'mapred', group: 'mapred', recurse: 'yes', mode: '0700' }
-     - { state: 'directory', path: '/data/1/mapred/local', owner: 'mapred', group: 'mapred', recurse: 'yes', mode: '0700' }
+     - { state: 'directory', path: '/data/1/mapred', owner: 'mapred', group: 'mapred', recurse: 'yes', mode: '0754' }
+     - { state: 'directory', path: '/data/1/mapred/local', owner: 'mapred', group: 'mapred', recurse: 'yes', mode: '0754' }
      - { state: 'directory', path: '/tmp/hadoop-mapred', owner: 'mapred', group: 'mapred', recurse: 'yes', mode: '0777' }
 
 - name:  Set up SeqWare directories

roles/seqware-helloworld/vars/main.yml

@@ -5,7 +5,7 @@
 # not sure about the best way of making sure both have the same defaults
 # however, a command-line variable overrides both at the same time
 seqware_provider: "artifactory"
-seqware_version: "1.0.14"
+seqware_version: "1.1.0"
 
 # variable specific to this role
 helloworld_s3_location: "https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_{{ seqware_version }}.zip"

roles/seqware-master-infrastructure/files/cloudera.pref

@@ -0,0 +1,3 @@
+Package: *
+Pin: release o=Cloudera, l=Cloudera
+Pin-Priority: 501

roles/seqware-master-infrastructure/tasks/main.yml

@@ -1,6 +1,11 @@
 ---
 # file: roles/seqware-master-infrastructure/tasks/main.yml
 
+- name: Setup cloudera preference
+  copy:
+    src: cloudera.pref
+    dest: /etc/apt/preferences.d/cloudera.pref
+
 - name:  Install Hadoop for a master
   apt: name={{ item }} state=present update_cache=yes cache_valid_time=3600
   register: oozie_installed
@@ -156,6 +161,7 @@
   service: name=hadoop-0.20-mapreduce-jobtracker state=started
 
 - name:  Start TaskTracker
+  sudo: True
   service: name=hadoop-0.20-mapreduce-tasktracker state=started
   when: single_node
 
@@ -173,7 +179,7 @@
   notify: restart oozie
   command: "{{ item }}"
   with_items:
-    - wget -q http://extjs.com/deploy/ext-2.2.zip
+    - wget -q http://archive.cloudera.com/gplextras/misc/ext-2.2.zip
     - unzip ext-2.2.zip
     - mv ext-2.2 /var/lib/oozie/
 
@@ -289,9 +295,17 @@
   command: exportfs -ra
   when: nfs_setup.changed
 
+- name:  NFS Restart
+  service: name=rpcbind state=restarted
+  when: nfs_setup.changed
+  ignore_errors: yes
+  when: ansible_distribution == 'Ubuntu' and ansible_distribution_release == 'trusty'
+
 - name:  NFS Restart
   service: name=portmap state=restarted
   when: nfs_setup.changed
+  ignore_errors: yes
+  when: ansible_distribution == 'Ubuntu' and ansible_distribution_release == 'precise'
 
 - name:  NFS Restart
   service: name=nfs-kernel-server state=restarted