smrt-analysis setup playbook

smrt-analysis.yml

- name: Configure smrt-analysis.las.iastate.edu
  hosts: smrt-analysis.las.iastate.edu
  user: root
  connection: smart

  vars_files:
    - ../vars/ISU/globals.yml
    - ../vars/directories.yml

  environment:
    SMRT_ROOT: "{{smrt_root}}"
    SMRT_USER: "{{smrt_user}}"
    SMRT_GROUP: "{{smrt_group}}"

  pre_tasks:
    - name: Create group of user to run smrt process
      group:
        name: "{{smrt_group}}"
        state: present
    - name: Create user to run smrt process
      user:
        name: "{{smrt_user}}"
        comment: "SMRT Analysis"
        group: "{{smrt_group}}"
        createhome: yes

  roles:
    - firewall
    - epel

  tasks:
    - name: Ensure environmet set for smrt
      lineinfile:
        dest: "/home/{{smrt_user}}/.bashrc"
        state: present
        line: "export SMRT_ROOT=\"{{smrt_root}}\""
    - name: Ensure environmet set for smrt
      lineinfile:
        dest: "/home/{{smrt_user}}/.bashrc"
        state: present
        line: "export SMRT_USER=\"{{smrt_user}}\""
    - name: Ensure environmet set for smrt
      lineinfile:
        line: "export SMRT_GROUP=\"{{smrt_group}}\""
        state: present
        dest: "/home/{{smrt_user}}/.bashrc"

    - name: Install redhat-lsb
      yum: name=redhat-lsb state=present
    - name: Install pip
      yum: name=python2-pip state=present
    - name: Installing pexpect from pip since titan version is less than what is required
      command: pip install pexpect

    - name: Create application directory
      file:
        path: "{{smrt_root}}"
        mode: u=rwx,g=rwx,o=r
        state: directory
        recurse: yes
        group: "{{smrt_group}}"
        owner: "{{smrt_user}}"

    - name: Download SMRT
      get_url:
        url: "{{ item.url }}"
        dest: "{{ item.dest }}"
        mode: 0755
        owner: "{{smrt_user}}"
        group: "{{smrt_group}}"
      with_items:
        - { url: 'https://s3.amazonaws.com/files.pacb.com/software/smrtanalysis/2.3.0/smrtanalysis_2.3.0.140936.run' , dest: '/tmp/smrtanalysis_2.3.0.140936.run' }
        - { url: 'https://s3.amazonaws.com/files.pacb.com/software/smrtanalysis/2.3.0/smrtanalysis-patch_2.3.0.140936.p5.run' , dest: '/tmp/smrtanalysispatch_2.3.0.140936.p5.run' }

    # Message incase application gets stuck in loop because of unanswered question caught by another regular expression.
    - name: Message
      vars:
        msg: |
             Warning: This installation is not smart enough to realize there is a infinite look with the answers since questions are looked for in regex expressions:
             Please run the following command as user: {{smrt_user}} should installation fail
             command: /tmp/smrtanalysis_2.3.0.140936.run -p /tmp/smrtanalysispatch_2.3.0.140936.p5.run --rootdir $SMRT_ROOT
      debug:
        msg: "{{ msg.split('\n') }}"

    - name: Installing smrtanalysis
      expect:
        command: /tmp/smrtanalysis_2.3.0.140936.run -p /tmp/smrtanalysispatch_2.3.0.140936.p5.run --rootdir {{smrt_root}}
        responses:
          # Asks for smrt_user since we are switchings to smrt_user using that variable . try .+
          (?i)Use the \'.+\' as the SMRT Analysis user\? \[Y/n\]\:: "Y"
          # Warning will appear no matter if min requirement is matched since rhel 7 is not supported yet
          (?i)Continue the installation\? \[Y/n\]\:: "Y"
          # Asking for DNS names
          (?i)Choice \[1\]\::
            - "1"
            - "4"
          # Additional DNS names
          (?i)Specify the DNS name\:: "{{smrt_host}}"
          # SMRT Analysis TomCat port and shutdownport
          (?i)Enter the \'main\' port for the SMRT Analysis Tomcat Webserver \[8080\]\:: {{smrt_port}}
          (?i)Enter the \'shutdown\' port for the SMRT Analysis Tomcat Webserver \[8005\]\:: "8005"
          # TMP dir
          # Enter the symlink destination for the TMP directory [/tmp/smrtanalysis]
          (?i)Enter the symlink destination for the TMP directory .+$: "/tmp/smrtanalysis"
          # UAERDATA Directory Setup Messages askes for storage to be above 500 GB
          (?i)Create this directory and continue with installation\? \[Y/n\]\:: "Y"
          # If older data directory present keep
          (?i)Keep this directory and continue with installation\? \[Y\/n\]\:: "Y"
          # Self contained mysql port then create mysql db
          (?i)Enter the mysql port \[53306\]\:: "53306"
          (?i)Ready to create internal database\.  Continue\? \[Y/n\]\:: "Y"
          # (?i)4\) NONE\\nChoice \[1\]\:: "4"
          (?i)Specify number of processors to use for parallel operations \(max.+$: {{smrt_procs}}
        timeout: 300
      become: yes
      become_user: "{{smrt_user}}"

    - name: Run SMRT
      command: $SMRT_ROOT/admin/bin/smrtportald-initd start
      become: yes
      become_user: "{{smrt_user}}"

    - name: Run SMRT
      command: $SMRT_ROOT/admin/bin/kodosd start
      become: yes
      become_user: "{{smrt_user}}"

    # Message incase application gets stuck in loop because of unanswered question caught by another regular expression.
    - name: Message
      vars:
        msg: |
             Installation complete application is running on port {{smrt_port}}
      debug:
        msg: "{{ msg.split('\n') }}"