AustralianBioCommons · eileen-xue · Apr 1, 2026 · Apr 1, 2026 · Apr 1, 2026 · Apr 2, 2026
diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@ For most users, a small Ubuntu VM inside OpenStack is the simplest and most repr
 Recommended head VM characteristics:
 
 ```
-Operating System: Ubuntu LTS (20.04 or newer)
+Operating System: Ubuntu LTS (24.04 or newer)
 CPU/RAM: minimal (e.g. 1–2 vCPUs, 2–4 GB RAM)
 Access: SSH enabled via key pair
 ```
@@ -55,7 +55,7 @@ The following steps describe how to create a head VM using the generic OpenStack
 ### Select the Source Image (Operating System)
 
 1. In the source tab, Select Boot Source: Image
-2. Choose a supported Ubuntu image (eg. Ubuntu 22.04)
+2. Choose a supported Ubuntu image (eg. Ubuntu 24.04)
 3. If the BioShell image has been previously built you should be able to select BioShell at this step.
 
 ### Choose an Instance Flavor
@@ -199,9 +199,9 @@ packer init .
 
 ### Step 2: Prepare Packer build configuration
 
-Before running the build, review and update `openstack-bioshell.pkr.hcl` to ensure the values match your OpenStack environment. If using a prepared config skip to step 3.
+Before running the build, review and update `[platform_name].pkrvars.hcl` to ensure the values match your OpenStack environment. If using a prepared config skip to step 3.
 
-**Note: Example working configurations for [Nectar](build/examples/openstack-bioshell-nectar.pkr.hcl) and [Nirin](build/examples/openstack-bioshell-nirin.pkr.hcl) are included and were last successfully tested on 2 February 2026. The Nirin configuration requires you to add your project [network](#network-cloud-dependant).**
+**Note: Example working configurations for [Nectar](build/packer-vars/nectar.pkrvars.hcl) and [Nirin](build/packer-vars/nirin.pkrvars.hcl) are included and were last successfully tested on 2 February 2026. The Nirin configuration requires you to add your project [network](#network-cloud-dependant).**
 
 At a minimum, check the following fields in the `source "openstack"` block:
 #### Source Image (Base OS)
@@ -214,7 +214,7 @@ Example output:
 +--------------------------------------+-------------------------------+--------+
 | ID                                   | Name                          | Status |
 +--------------------------------------+-------------------------------+--------+
-| <uuid>                               | Ubuntu 20.04                  | active |
+| <uuid>                               | Ubuntu 24.04                  | active |
 +--------------------------------------+-------------------------------+--------+
 ```
 Copy the ID of the image you want to use and set it as:
@@ -284,29 +284,26 @@ If your cloud has a default network, this field may be omitted.
 
 #### CVMFS Configuration
 
-The [`build-bioshell.yml`](build/build-bioshell.yml) playbook configures CVMFS for the image.  
+The [`ansible cvmfs role`](build/ansible/roles/cvmfs/tasks/main.yml) configures CVMFS for the image.  
 
 - By default, the CVMFS HTTP proxy is set to **DIRECT** to make the build more portable across environments.  
-- If a infrastructure specific proxy is available (eg. `http://cvmfs-proxy-1.nci.org.au:3128;http://cvmfs-proxy-2.nci.org.au:3128` on Nirin), update the `CVMFS_HTTP_PROXY` line in the playbook.
+- If a infrastructure specific proxy is available (eg. `http://cvmfs-proxy-1.nci.org.au:3128;http://cvmfs-proxy-2.nci.org.au:3128` on Nirin), add new file `[platform_name].yml` to [`ansible vars`](build/ansible/vars/) with `cvmfs_proxy: [proxy]`.
 
-The relevant task in the playbook:
-
-```yaml
-- 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
-```
 ### Step 3: Build BioShell
 Once the configuration has been updated, run the build:
 
+For Nirin and Nectar users:
+```
+./scripts/nirin.sh      // nirin users
+./scripts/nectar.sh.    // nectar users
 ```
-packer build openstack-bioshell.pkr.hcl
+For other platform users:
 ```
+packer build \
+  -var-file="./packer-vars/[platform_name].pkrvars.hcl" \
+  ./openstack-bioshell.pkr.hcl
+```
+
 ### Step 4: Verify Image
 After the build process is complete, verify the newly created image by running:
 ```
@@ -364,7 +361,6 @@ This image uses CernVM-FS (CVMFS) to provide access to shared bioinformatics sof
 
 Access CVMFS repositories:
 ```
-ls /cvmfs/data.biocommons.aarnet.edu.au
 ls /cvmfs/data.galaxyproject.org
 ls /cvmfs/singularity.galaxyproject.org
 

diff --git a/build/ansible/build-bioshell.yml b/build/ansible/build-bioshell.yml
@@ -0,0 +1,16 @@
+---
+- name: Build BioShell base image
+  hosts: all
+  become: true
+
+  vars_files:
+    - "vars/tool-versions.yml"
+    - "vars/{{ platform }}.yml"
+
+  roles:
+    - common
+    - singularity
+    - nextflow
+    - rstudio
+    - cvmfs
+    - shelley-bio
diff --git a/build/ansible/roles/common/tasks/main.yml b/build/ansible/roles/common/tasks/main.yml
@@ -0,0 +1,201 @@
+---
+- name: Wait for apt lock
+  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 cache
+  apt:
+    update_cache: yes
+  register: apt_update
+  retries: 3
+  delay: 10
+  until: apt_update is succeeded
+
+- name: Install base packages
+  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 R build dependencies
+  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
+
+- 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
+
+- name: Ensure module directories exist
+  file:
+    path: "{{ item }}"
+    state: directory
+  loop:
+    - "{{ module_base_opt }}"
+    - "{{ module_base_apps }}"
+
+- name: Create /apps symlinks and paths
+  shell: |
+    mkdir -p /apps/R/{{ r_version }}/bin /apps/Modules/modulefiles/R
+    ln -sf /usr/bin/R /apps/R/{{ r_version }}/bin/R
+
+    mkdir -p /apps/jupyter/{{ jupyter_version }}/bin /apps/Modules/modulefiles/jupyter
+    ln -sf /usr/bin/jupyter /apps/jupyter/{{ jupyter_version }}/bin/jupyter
+
+    mkdir -p /apps/snakemake/{{ snakemake_version }}/bin /apps/Modules/modulefiles/snakemake
+    ln -sf /usr/bin/snakemake /apps/snakemake/{{ snakemake_version }}/bin/snakemake
+
+    mkdir -p /apps/ansible/{{ ansible_version.string }}/bin /apps/Modules/modulefiles/ansible
+    ln -sf /usr/bin/ansible /apps/ansible/{{ ansible_version.string }}/bin/ansible
+
+  args:
+    executable: /bin/bash
+
+- name: Update PATH in /etc/environment
+  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('^:|:$', '') }}:/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:
+    - "{{ module_base_apps }}"
+    - "{{ module_base_opt }}"
+
+- name: Create jupyter modulefile
+  copy:
+    dest: "/apps/Modules/modulefiles/jupyter/{{ jupyter_version }}"
+    content: |
+      #%Module1.0
+
+      prepend-path PATH "/apps/jupyter/{{ jupyter_version }}/bin"
+
+- name: Create snakemake modulefile
+  copy:
+    dest: "/apps/Modules/modulefiles/snakemake/{{ snakemake_version }}"
+    content: |
+      #%Module1.0
+
+      prepend-path PATH "/apps/snakemake/{{ snakemake_version }}/bin"
+
+- name: Create R modulefile
+  copy:
+    dest: "/apps/Modules/modulefiles/R/{{ r_version }}"
+    content: |
+      #%Module1.0
+
+      prepend-path PATH "/apps/R/{{ r_version }}/bin"
+
+- name: Create ansible modulefile
+  copy:
+    dest: "/apps/Modules/modulefiles/ansible/{{ ansible_version.string }}"
+    content: |
+      #%Module1.0
+
+      prepend-path PATH "/apps/ansible/{{ ansible_version.string }}/bin"
+
+- name: Ensure motd.d directory exists
+  file:
+    path: /etc/motd.d
+    state: directory
+    mode: '0755'
+
+- name: Add BioShell welcome message with turtle
+  copy:
+    dest: /etc/motd.d/bioshell
+    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                                        #
+      ##################################################################