build-bioshell.yml

---
- name: Build BioShell
  hosts: all
  become: true

  tasks:
    - name: Wait for apt lock to be released
      become: true
      shell: |
        while fuser /var/lib/apt/lists/lock >/dev/null 2>&1 || \
              fuser /var/lib/dpkg/lock-frontend >/dev/null 2>&1 || \
              fuser /var/lib/dpkg/lock >/dev/null 2>&1; do
          sleep 5
        done
      changed_when: false

    - name: Update apt repository
      apt:
        update_cache: yes
      register: apt_update
      retries: 3
      delay: 10
      until: apt_update is succeeded

    - name: Ensure necessary packages are installed
      apt:
        name:
          - lmod
          - build-essential
          - libssl-dev
          - uuid-dev
          - libgpgme11-dev
          - squashfs-tools
          - git
          - wget
          - autoconf
          - automake
          - cryptsetup
          - fuse2fs
          - fuse
          - libfuse-dev
          - libglib2.0-dev
          - libtool
          - pkg-config
          - runc
          - squashfs-tools-ng
          - uidmap
          - zlib1g-dev
          - libseccomp-dev
          - nano
          - jupyter
          - snakemake
          - r-base
          - python3
          - python3-pip
          - python3-venv
          - ansible
          - tree
        state: present

    - name: Install build dependencies for R packages
      apt:
        name:
          - build-essential
          - cmake
          - gdal-bin
          - libcurl4-openssl-dev
          - libxml2-dev
          - libfontconfig1-dev
          - libfreetype6-dev
          - libharfbuzz-dev
          - libfribidi-dev
          - libudunits2-dev
          - libglpk-dev
          - libblas-dev
          - liblapack-dev
          - libopenblas-dev
          - libtiff5-dev
          - libjpeg-dev
          - libpng-dev
          - libcairo2-dev
        state: present
        update_cache: yes

    - name: Ensure the /opt/Modules/modulefiles directory exists
      file:
        path: /opt/Modules/modulefiles
        state: directory

    - name: Ensure the /apps/Modules/modulefiles directory exists
      file:
        path: /apps/Modules/modulefiles
        state: directory
    
    # Install RStudio
    - name: Install RStudio Server dependencies
      apt:
        name:
          - gdebi-core
          - libclang-dev
        state: present

    - name: Set RStudio Server version
      set_fact:
        rstudio_version: "2023.12.1-402"

    - name: Download RStudio Server
      get_url:
        url: "https://download2.rstudio.org/server/jammy/amd64/rstudio-server-{{ rstudio_version }}-amd64.deb"
        dest: "/tmp/rstudio-server.deb"

    - name: Install RStudio Server
      apt:
        deb: /tmp/rstudio-server.deb

    - name: Clean up RStudio Server installer
      file:
        path: /tmp/rstudio-server.deb
        state: absent

    - name: Enable and start RStudio Server
      systemd:
        name: rstudio-server
        enabled: no
        state: stopped

    # Install Singularity
    - name: Check if /apps/go exists
      stat:
        path: /apps/go
      register: go_apps_dir

    - name: Check if /usr/local/go exists
      stat:
        path: /usr/local/go
      register: go_local_dir

    - name: Report status of /apps/go
      debug:
        msg: "/apps/go exists: {{ go_apps_dir.stat.exists }}"

    - name: Report status of /usr/local/go
      debug:
        msg: "/usr/local/go exists: {{ go_local_dir.stat.exists }}"

    - name: Take action based on Go installation paths
      debug:
        msg: >
          Go is installed in:
          {% if go_apps_dir.stat.exists %}
            - /apps/go
          {% endif %}
          {% if go_local_dir.stat.exists %}
            - /usr/local/go
          {% endif %}
          {% if not (go_apps_dir.stat.exists or go_local_dir.stat.exists) %}
            - Neither path exists.
          {% endif %}

    - name: Install Go
      block:
        - name: Set Go version and architecture
          set_fact:
            go_version: "1.22.7"
            os: "linux"
            arch: "amd64"

        - name: Download Go binary
          get_url:
            url: "https://dl.google.com/go/go{{ go_version }}.{{ os }}-{{ arch }}.tar.gz"
            dest: /tmp/go{{ go_version }}.{{ os }}-{{ arch }}.tar.gz

        - name: Extract Go binary to  /apps/
          unarchive:
            src: /tmp/go{{ go_version }}.{{ os }}-{{ arch }}.tar.gz
            dest: /apps/
            remote_src: yes

    - name: Create directories for Singularity 
      shell: |
        export VERSION=4.2.1 && \
        export GOPATH=${HOME}/go && \
        mkdir -p $GOPATH/src/github.com/sylabs && \
        cd $GOPATH/src/github.com/sylabs && \
        wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
        tar -xzf singularity-ce-${VERSION}.tar.gz && \
        cd ./singularity-ce-${VERSION}

    - name: Compile the SingularityCE source code
      shell: |
        export VERSION=4.2.1  
        export GOPATH=${HOME}/go 
        export PATH=/apps/go/bin:${PATH}:${GOPATH}/bin
        cd $GOPATH/src/github.com/sylabs/singularity-ce-${VERSION} && \
        ./mconfig --prefix=/opt/singularity/4.2.1 && \
        make -C ./builddir && \
        make -C ./builddir install
      args:
        executable: /bin/bash

    - name: Clean up Singularity source code
      file:
        path: /tmp/singularity
        state: absent
    
    - name: Clean up go source code
      file:
        path: /apps/go
        state: absent

    - name: Create modulefile for Singularity
      copy:
        dest: /opt/Modules/modulefiles/singularity
        content: |
          #%Module1.0

          proc ModulesHelp { } {
              puts stderr "\tThis module makes available commands to run Singularity\n"
          }

          module-whatis   "Sets up the Singularity system in your environment"
          prepend-path PATH "/opt/singularity/4.2.1/bin"

    # Install Spack
    - name: Install Spack
      block:
        - name: Clone Spack repository
          shell: |
            git clone -c feature.manyFiles=true --depth=2 https://github.com/spack/spack.git /usr/local/spack

    # Intall Nextflow
    - name: Install Java 21 (required for Nextflow)
      apt:
        name: openjdk-21-jdk
        state: present
      become: yes
      when: ansible_os_family == "Debian"

    - name: Ensure Java 21 is default JVM
      alternatives:
        name: java
        path: /usr/lib/jvm/java-21-openjdk-amd64/bin/java
      become: yes
      when: ansible_os_family == "Debian"


    # Make Nextflowfolder
    - name: Create Nextflow folder
      shell: |
        mkdir -p /apps/Modules/modulefiles/nextflow
        mkdir -p /apps/nextflow/24.10.2/bin
      args:
        executable: /bin/bash

    - name: Download Nextflow
      get_url:
        url: https://get.nextflow.io
        dest: /tmp/nextflow
        mode: '0755'

    - name: Move Nextflow to /apps
      copy:
        src: /tmp/nextflow
        dest: /apps/nextflow/24.10.2/bin
        mode: '0755'
        remote_src: yes

    - name: Verify Nextflow installation with user-writable paths
      shell: |
          export NXF_VER=24.10.2
          export NXF_AUTOINSTALL=false
          export NXF_DIST=$HOME/nextflow/framework
          export CAPSULE_CACHE_DIR=$HOME/nextflow/capsule
          export PATH=/apps/nextflow/24.10.2/bin:${PATH}
          mkdir -p "$NXF_DIST" "$CAPSULE_CACHE_DIR"
          nextflow -version
      register: nextflow_version
      args:
        executable: /bin/bash

    - name: Clean up temporary files
      file:
        path: /tmp/nextflow
        state: absent

    - name: Create modulefile for Nextflow
      copy:
        dest: /apps/Modules/modulefiles/nextflow/24.10.2
        content: |
          #%Module1.0

          module-whatis   "Nextflow"
          prepend-path PATH "/apps/nextflow/24.10.2/bin"
          setenv NXF_DIST /apps/nextflow/24.10.2/framework
          setenv CAPSULE_CACHE_DIR /apps/nextflow/24.10.2/capsule

    # add nf-core modulefile
    - name: Create nf-core install directory
      file:
        path: /apps/nf-core/3.5.2
        state: directory
        recurse: yes
    
    - name: Install Python venv dependency
      apt:
        name: python3-venv
        state: present
        update_cache: yes

    - name: Create nf-core virtual environment
      command: python3 -m venv /apps/nf-core/3.5.2
      args:
        creates: /apps/nf-core/3.5.2/bin/activate

    - name: Install nf-core into venv
      command: /apps/nf-core/3.5.2/bin/pip install nf-core==3.5.2

    - name: Create symlink for nfcore alias (optional)
      file:
        src: /apps/nf-core/3.5.2/bin/nf-core
        dest: /apps/nf-core/3.5.2/bin/nfcore
        state: link

    # ---------------------------
    # Create modulefile directory
    # ---------------------------

    - name: Create nf-core modulefile directory
      file:
        path: /apps/Modules/modulefiles/nf-core
        state: directory

    - name: Create nf-core modulefile
      copy:
        dest: /apps/Modules/modulefiles/nf-core/3.5.2
        content: |
          #%Module1.0
          module-whatis "nf-core 3.5.2"
          prepend-path PATH "/apps/nf-core/3.5.2/bin"

          if { [ module-info mode load ] } {
              module load nextflow
          }

    # Install shpc
    - name: Install shpc
      shell: |
        mkdir -p /opt/shpc/bin
        cd /opt/shpc
        git clone -b 0.1.28 https://github.com/singularityhub/singularity-hpc.git
        cd singularity-hpc
        pip install -e .[all]
        ln -s /opt/shpc/bin/shpc /usr/local/bin/shpc
        cp /opt/shpc/singularity-hpc/shpc/settings.yml /opt/shpc/singularity-hpc/shpc/settings-default.yml 
        cp /opt/shpc/singularity-hpc/shpc/main/modules/templates/singularity.lua /opt/shpc/singularity-hpc/shpc/main/modules/templates/singularity-original.lua

    - name: update module_base
      lineinfile:
        path: /opt/shpc/singularity-hpc/shpc/settings.yml
        regexp: '^module_base: \$root_dir/modules'  
        line: 'module_base: $HOME/shpc/modules' 
        state: present 

    - name: update container_base
      lineinfile:
        path: /opt/shpc/singularity-hpc/shpc/settings.yml
        regexp: '^container_base: \$root_dir/containers' 
        line: 'container_base: $HOME/shpc/containers' 
        state: present  

    - name: update wrapper_base
      lineinfile:
        path: /opt/shpc/singularity-hpc/shpc/settings.yml
        regexp: '^wrapper_base: \$root_dir/modules'  
        line: 'wrapper_base: $HOME/shpc/wrappers' 
        state: present

    - name: update view_base
      lineinfile:
        path: /opt/shpc/singularity-hpc/shpc/settings.yml
        regexp: '^views_base: \$root_dir/views'  
        line: 'views_base: $HOME/shpc/views' 
        state: present

    - name: Check if singularity.lua exists
      stat:
        path: "/opt/shpc/singularity-hpc/shpc/main/modules/templates/singularity.lua"
      register: lua_file

    - name: Create singularity.lua if it does not exist
      copy:
        dest: "/opt/shpc/singularity-hpc/shpc/main/modules/templates/singularity.lua"
        content: |
          -- Default content for singularity.lua
          local moduleDir = subprocess("realpath " .. myFileName()):match("(.*[/])") or "."
      when: not lua_file.stat.exists

    - name: Replace line starting with 'local moduleDir'
      lineinfile:
        path: "/opt/shpc/singularity-hpc/shpc/main/modules/templates/singularity.lua"
        regexp: '^local moduleDir.*'  
        line: 'local moduleDir = myFileName():match("(.*[/])") or "."' 
        state: present
    
    - name: Create shpc modulefile
      copy:
        dest: "/opt/Modules/modulefiles/shpc"
        content: |
          #%Module1.0

          module-whatis   "Singularity HPC"
          prepend-path PATH "/opt/shpc/bin"
          if { [ module-info mode load ] } {
            module load singularity
          }


    - name: Create /apps paths and symlink system binaries
      shell: |
        mkdir -p /apps/R/4.1.2/bin /apps/Modules/modulefiles/R
        ln -sf /usr/bin/R /apps/R/4.1.2/bin/R

        mkdir -p /apps/jupyter/2024.10/bin /apps/Modules/modulefiles/jupyter
        ln -sf /usr/bin/jupyter /apps/jupyter/2024.10/bin/jupyter

        mkdir -p /apps/snakemake/6.15.1/bin /apps/Modules/modulefiles/snakemake
        ln -sf /usr/bin/snakemake /apps/snakemake/6.15.1/bin/snakemake

        mkdir -p /apps/ansible/2.10.8/bin /apps/Modules/modulefiles/ansible
        ln -sf /usr/bin/ansible /apps/ansible/2.10.8/bin/ansible


        mkdir -p /apps/RStudio/2023.12.1/bin /apps/Modules/modulefiles/rstudio
        ln -sf /usr/sbin/rstudio-server /apps/RStudio/2023.12.1/bin/rstudio-server
      args:
        executable: /bin/bash


    - name: Create R modulefile
      copy:
        dest: "/apps/Modules/modulefiles/R/4.1.2"
        content: |
          #%Module1.0

          prepend-path PATH "/apps/R/4.1.2/bin"
        
    - name: Create jupyter modulefile
      copy:
        dest: "/apps/Modules/modulefiles/jupyter/2024.10"
        content: |
          #%Module1.0

          prepend-path PATH "/apps/jupyter/2024.10/bin"


    - name: Create snakemake modulefile
      copy:
        dest: "/apps/Modules/modulefiles/snakemake/6.15.1"
        content: |
          #%Module1.0

          prepend-path PATH "/apps/snakemake/6.15.1/bin"

    - name: Create R modulefile
      copy:
        dest: "/apps/Modules/modulefiles/ansible/2.10.8"
        content: |
          #%Module1.0

          prepend-path PATH "/apps/ansible/2.10.8/bin"

    - name: Create RStudio modulefile
      become: yes
      copy:
        dest: "/apps/Modules/modulefiles/rstudio/2023.12.1"
        owner: root
        group: root
        mode: '0644'
        content: |
          #%Module1.0
          module-whatis "RStudio Server 2023.12.1"
          prepend-path PATH "/usr/lib/rstudio-server/bin:/usr/lib/rstudio-server/bin"

          
          set ip [exec /bin/bash -c "
            curl -fsS --max-time 0.5 http://169.254.169.254/latest/meta-data/public-ipv4 2>/dev/null || true
          "]

          if { $ip eq "" } {
            set ip [exec /bin/bash -c "hostname -I 2>/dev/null | awk '{print \$1}'"]
          }

          puts stderr ""
          puts stderr "RStudio Server"
          puts stderr "----------------------------------"
          puts stderr "Login Details:"
          puts stderr ""
          puts stderr "  Username: $env(USER)"
          puts stderr "  Password: Your Linux account password"
          puts stderr ""
          puts stderr "If you have not set a password yet, run:"
          puts stderr ""
          puts stderr "  sudo passwd $env(USER)"
          puts stderr ""
          puts stderr "To start RStudio Server:"
          puts stderr ""
          puts stderr "  sudo rstudio-server start"
          puts stderr ""
          puts stderr "Then open in your browser:"
          puts stderr ""
          puts stderr "  http://$ip:8787"
          puts stderr ""

     
    #Install cvmfs and configure with Galaxy, AARNET training, EESSI access
    - name: Download CVMFS release package
      get_url:
        url: https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb
        dest: /tmp/cvmfs-release-latest_all.deb

    - name: Install CVMFS release package
      apt:
        deb: /tmp/cvmfs-release-latest_all.deb

    - name: Remove CVMFS release package
      file:
        path: /tmp/cvmfs-release-latest_all.deb
        state: absent

    - name: Update apt cache
      apt:
        update_cache: yes

    - name: Install CVMFS
      apt:
        name: cvmfs
        state: present

    - name: Write default.local
      copy:
        dest: /etc/cvmfs/default.local
        content: |
          CVMFS_REPOSITORIES=data.biocommons.aarnet.edu.au,data.galaxyproject.org,singularity.galaxyproject.org
          CVMFS_HTTP_PROXY='DIRECT'
          CVMFS_QUOTA_LIMIT=4096
          CVMFS_USE_GEOAPI=yes

    - name: set up cvmfs and set autofs
      shell: |
          cvmfs_config setup
          sed -i 's%#+dir:/etc/auto.master.d%+dir:/etc/auto.master.d%' /etc/auto.master
          systemctl restart autofs

    - name: Write data.biocommons.aarnet.edu.au.conf 
      copy:
        dest: /etc/cvmfs/config.d/data.biocommons.aarnet.edu.au.conf
        content: |
          CVMFS_SERVER_URL="http://bcws.test.aarnet.edu.au/cvmfs/@fqrn@"
          CVMFS_PUBLIC_KEY="/etc/cvmfs/keys/data.biocommons.aarnet.edu.au/data.biocommons.aarnet.edu.au.pub"

    - name: Write galaxyproject.org.conf 
      copy:
        dest: /etc/cvmfs/domain.d/galaxyproject.org.conf 
        content: |
          CVMFS_SERVER_URL="http://cvmfs1-tacc0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-iu0.galaxyproject.org/cvmfs/@fqrn@;http://cvmfs1-psu0.galaxyproject.org/cvmfs/@fqrn@;http://galaxy.jrc.ec.europa.eu:8008/cvmfs/@fqrn@;http://cvmfs1-mel0.gvl.org.au/cvmfs/@fqrn@"
          CVMFS_KEYS_DIR="/etc/cvmfs/keys/galaxyproject.org"

    - name: Ensure the /etc/cvmfs/keys/data.biocommons.aarnet.edu.au directory exists
      file:
        path: /etc/cvmfs/keys/data.biocommons.aarnet.edu.au
        state: directory
        
    - name: data.biocommons.aarnet.edu.au key
      copy:
        dest: /etc/cvmfs/keys/data.biocommons.aarnet.edu.au/data.biocommons.aarnet.edu.au.pub
        content: |
          -----BEGIN PUBLIC KEY-----
          MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA3JEVgVhOjigVTX4OPVpj
          EPIZEuhGzqhuvzu4ujovyEjrYoeXIfG+YSFIj9a3YxgPxRl1LVsBm59g+tqrUs25
          //xUFIQVomaw8gLRy9txflDe2SWVh4m40IIEGGQQoXyY/Iv26i8vtcVhAJnvL+lM
          Iu25nG3MM8rcuuGrYnQQekeoSZLd5Tg4JHC+YEy9n1jUkxCBUTr5XFIXCEQkR2Nr
          9p6Hgol/NqUKZT76K3yWNfbRS/kXEB3ZOP6h0QDvVgwzfgTifoLge1cfJuiy/KtM
          /UJr1k/cVp4l5ssL7Qqx582eGRJ/rn7K2BVNVF8XI+Fvgpp9DQPxu6U4S4WANKBE
          OQIDAQAB
          -----END PUBLIC KEY-----

    - name: Ensure the /etc/cvmfs/keys/galaxyproject.org exists
      file:
        path: /etc/cvmfs/keys/galaxyproject.org
        state: directory


    - name: Write data.galaxyproject.org key
      copy:
        dest: /etc/cvmfs/keys/galaxyproject.org/data.galaxyproject.org.pub 
        content: |
          -----BEGIN PUBLIC KEY-----
          MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA5LHQuKWzcX5iBbCGsXGt
          6CRi9+a9cKZG4UlX/lJukEJ+3dSxVDWJs88PSdLk+E25494oU56hB8YeVq+W8AQE
          3LWx2K2ruRjEAI2o8sRgs/IbafjZ7cBuERzqj3Tn5qUIBFoKUMWMSIiWTQe2Sfnj
          GzfDoswr5TTk7aH/FIXUjLnLGGCOzPtUC244IhHARzu86bWYxQJUw0/kZl5wVGcH
          maSgr39h1xPst0Vx1keJ95AH0wqxPbCcyBGtF1L6HQlLidmoIDqcCQpLsGJJEoOs
          NVNhhcb66OJHah5ppI1N3cZehdaKyr1XcF9eedwLFTvuiwTn6qMmttT/tHX7rcxT
          owIDAQAB
          -----END PUBLIC KEY-----

    - name: Write singularity.galaxyproject.org.pub key
      copy:
        dest: /etc/cvmfs/keys/galaxyproject.org/singularity.galaxyproject.org.pub
        content: |
          -----BEGIN PUBLIC KEY-----
          MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAuJZTWTY3/dBfspFKifv8
          TWuuT2Zzoo1cAskKpKu5gsUAyDFbZfYBEy91qbLPC3TuUm2zdPNsjCQbbq1Liufk
          uNPZJ8Ubn5PR6kndwrdD13NVHZpXVml1+ooTSF5CL3x/KUkYiyRz94sAr9trVoSx
          THW2buV7ADUYivX7ofCvBu5T6YngbPZNIxDB4mh7cEal/UDtxV683A/5RL4wIYvt
          S5SVemmu6Yb8GkGwLGmMVLYXutuaHdMFyKzWm+qFlG5JRz4okUWERvtJ2QAJPOzL
          mAG1ceyBFowj/r3iJTa+Jcif2uAmZxg+cHkZG5KzATykF82UH1ojUzREMMDcPJi2
          dQIDAQAB
          -----END PUBLIC KEY-----

    - name: setup cvmfs and probe resources
      shell: |
          cvmfs_config setup
          cvmfs_config probe data.galaxyproject.org
          cvmfs_config probe singularity.galaxyproject.org

    - name: Update PATH to remove /usr/local/games and add /usr/local/spack/bin
      lineinfile:
        path: /etc/environment
        regexp: '^PATH='
        line: 'PATH="{{ updated_path }}"'
        state: present
      vars:
        current_path: "{{ ansible_env.PATH }}"
        updated_path: "{{ current_path | replace('/usr/local/games', '') | trim | replace('::', ':') | regex_replace('^:|:$', '') | regex_replace('^:', '') | regex_replace(':$', '') }}:/usr/local/spack/bin"

    - name: Comment out existing module paths
      lineinfile:
        path: /etc/lmod/modulespath
        regexp: '^(.*(/etc/lmod/modules|/usr/share/lmod/lmod/modulefiles).*)'
        line: '# \1'
        backrefs: yes
        state: present

    - name: Add new module paths
      lineinfile:
        path: /etc/lmod/modulespath
        line: "{{ item }}"
        state: present
      loop:
        - '/apps/Modules/modulefiles'
        - '/opt/Modules/modulefiles'

    # ==============================
    # Install Shelley Bio
    # ==============================
    - name: Ensure Python 3 and pip are installed
      apt:
        name:
          - python3
          - python3-pip
        state: present
        update_cache: yes

    - name: Ensure Git is installed
      apt:
        name: git
        state: present

    - name: Create installation directory for Shelley Bio
      file:
        path: /opt/shelley-bio
        state: directory
        owner: root
        group: root
        mode: '0755'

    - name: Clone Shelley Bio repository
      git:
        repo: https://github.com/Sydney-Informatics-Hub/shelley-bio.git
        dest: /opt/shelley-bio
        version: main
        force: yes
        depth: 1

    - name: Install Shelley Bio dependencies globally
      pip:
        requirements: /opt/shelley-bio/requirements.txt
        state: present
        executable: pip3

    - name: Install Shelley Bio package globally
      pip:
        name: /opt/shelley-bio
        editable: yes
        state: present
        executable: pip3


    - name: Create system-wide launcher script
      copy:
        dest: /usr/local/bin/shelley-bio
        owner: root
        group: root
        mode: '0755'
        content: |
          #!/usr/bin/env bash
          exec python3 -m shelley_bio.client.cli "$@"

    - name: Test Shelley Bio CLI
      command: shelley-bio search "quality control"
      register: shelley_cli_test
      ignore_errors: yes

    - name: Show Shelley Bio CLI test output
      debug:
        var: shelley_cli_test.stdout_lines

    - name: Add BioShell welcome message with turtle
      copy:
        dest: /etc/motd
        owner: root
        group: root
        mode: '0644'
        content: |
        ##################################################################
        #                                                                #
        # Welcome to BioShell!                                           #
        #                                                                #
        # A range of commonly used bioinformatics software is available  #
        # via CVMFS.                                                     #
        #                                                                #
        # To make the software folders visible, run:                     #
        #   cvmfs_config probe                                           #
        #                                                                #
        # If you need help finding and installing software,              #
        # ask Shelley-Bio                                                #
        #                      _   .----.                                #
        #                     (_ \/      \_,                             #
        #                        `uu----uu'                              #
        # Basic commands:                                                #
        # shelley-bio find <tool>                                        #
        # shelley-bio search "<function>"                                #
        # shelley-bio versions <tool>                                    #
        # shelley-bio build <tool>                                       #
        # shelley-bio interactive                                        #
        ##################################################################