playbook.yml

---
# run provision and build tasks on all hosts (various groups specified below)

# hosts: all handles tasks for all hosts and gets variables from all.yml
- name: Build environment for running bactopia
  hosts: all
  become: true
  vars_files:
      - "{{ inventory_dir }}/group_vars/all.yml"

  pre_tasks:
      - name: Get current server users
        ansible.builtin.getent:
            database: passwd
            fail_key: true

      - name: "Ensure bactopia service added to user: {{ bactopia_user }}"
        ansible.builtin.user:
            name: "{{ bactopia_user }}"
            shell: /sbin/nologin
            comment: "bactopia system user"
            state: present
        with_items: "{{ bactopia_user }}"
        when: bactopia_user not in ansible_facts.getent_passwd

      - name: Install git
        ansible.builtin.yum:
            name: git
            state: present

      - name: Install docker
        ansible.builtin.yum:
            name: docker
            state: present

      - name: "Add user to docker group: {{ bactopia_user }}"
        ansible.builtin.user:
            name: "{{ bactopia_user }}"
            append: true
            groups: docker

      - name: Enable and start docker service
        ansible.builtin.systemd:
            daemon_reload: true
            name: docker
            enabled: true
            state: started

      - name: Download Miniconda3
        ansible.builtin.get_url:
            url: https://repo.anaconda.com/miniconda/Miniconda3-py311_23.9.0-0-Linux-x86_64.sh
            dest: /tmp/install-miniconda3.sh
            checksum: sha256:43651393236cb8bb4219dcd429b3803a60f318e5507d8d84ca00dafa0c69f1bb
            mode: "0550"

      - name: Create conda folder
        become: true
        ansible.builtin.file:
            path: /opt/miniconda3
            state: directory
            owner: root
            mode: "0755"
            recurse: true

      - name: Install conda
        ansible.builtin.command: |
            /tmp/install-miniconda3.sh -b -u -p /opt/miniconda3
        changed_when: false

      - name: Remove conda installer
        ansible.builtin.file:
            state: absent
            path: /tmp/install-miniconda3.sh

      - name: Add conda bin to path on login
        ansible.builtin.lineinfile:
            path: /etc/profile
            line: "export PATH=/opt/miniconda3/bin:$PATH"
            create: true
            mode: "0644"

      - name: Initialize conda on login
        become: true
        ansible.builtin.file:
            src: /opt/miniconda3/etc/profile.d/conda.sh
            dest: /etc/profile.d/conda.sh
            state: link

      - name: Allow all to read conda folder
        become: true
        ansible.builtin.file:
            path: /opt/miniconda3
            mode: +r
            recurse: true

      - name: Allow execution for conda binaries
        become: true
        ansible.builtin.file:
            path: /opt/miniconda3/bin
            mode: +x
            recurse: true

      - name: Instantiate bactopia environment
        ansible.builtin.command: |
            bash -l -c 'conda create -n bactopia -c conda-forge -c bioconda bactopia -y'
        changed_when: false

      - name: Activate bactopia environment on login
        ansible.builtin.lineinfile:
            path: /etc/profile
            line: "conda activate bactopia"

      - name: Copy bactopia run script to the VM
        ansible.builtin.copy:
            src: files/run-bactopia-local.sh
            dest: /home/vagrant/run-bactopia-local.sh
            mode: "755"