├── ansible
    ├── playbooks
    │   └── sync_release.yml
    ├── inventory
    │   └── hosts.yml
    └── roles
    │   └── bioc_sync
    │       ├── templates
    │           └── paths.j2
    │       └── tasks
    │           └── main.yml
├── README.md
└── .github
    └── workflows
        └── sync-release.yml


/ansible/playbooks/sync_release.yml:
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1 | ---
2 | - name: Sync Bioconductor Release
3 |   hosts: bioc_vm
4 |   become: yes
5 |   vars:
6 |     bioc_version: "{{ biocver | default('3.19') }}"
7 |   roles:
8 |     - bioc_sync
9 | 


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/ansible/inventory/hosts.yml:
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1 | all:
2 |   hosts:
3 |     bioc_vm:
4 |       ansible_host: "{{ lookup('env', 'BIOC_VM_IP') }}"
5 |       ansible_user: ubuntu
6 |       ansible_ssh_private_key_file: "{{ lookup('env', 'SSH_KEY_PATH') }}"
7 | 


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/ansible/roles/bioc_sync/templates/paths.j2:
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 1 | {{ bioc_version }}/books/bin
 2 | {{ bioc_version }}/bioc/bin
 3 | {{ bioc_version }}/data/annotation/bin
 4 | {{ bioc_version }}/data/experiment/bin
 5 | {{ bioc_version }}/workflows/bin
 6 | {{ bioc_version }}/books/src
 7 | {{ bioc_version }}/bioc/src
 8 | {{ bioc_version }}/data/annotation/src
 9 | {{ bioc_version }}/data/experiment/src
10 | {{ bioc_version }}/workflows/src
11 | {{ bioc_version }}/BiocViews
12 | {{ bioc_version }}/BiocViews.html
13 | {{ bioc_version }}/index.html
14 | 


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/README.md:
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 1 | # Bioconductor Auto Archive Release
 2 | 
 3 | This repository contains automation scripts for archiving Bioconductor releases.
 4 | 
 5 | ## Required GitHub Secrets
 6 | 
 7 | - `BIOC_VM_IP`: IP address of the VM where the sync will run
 8 | - `VM_SSH_KEY`: SSH private key for accessing the VM
 9 | - `RSYNC_PRIVATE_KEY`: Private key for rsync authentication
10 | - `RCLONE_CONF_CONTENTS`: Complete rclone configuration file contents
11 | 
12 | 
13 | ## Usage
14 | 
15 | 1. Go to Actions tab
16 | 2. Select "Sync Bioconductor Release" workflow
17 | 3. Click "Run workflow"
18 | 4. Enter the Bioconductor version to sync
19 | 5. Click "Run workflow"
20 | 
21 | 


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/ansible/roles/bioc_sync/tasks/main.yml:
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 1 | ---
 2 | - name: Create work directory
 3 |   file:
 4 |     path: "/tmp/bioc_sync"
 5 |     state: directory
 6 |     mode: '0755'
 7 | 
 8 | - name: Copy rsync key
 9 |   copy:
10 |     content: "{{ lookup('env', 'RSYNC_PRIVATE_KEY') }}"
11 |     dest: "/tmp/bioc_sync/rsync-key.pem"
12 |     mode: '0600'
13 | 
14 | - name: Create temporary rclone config directory
15 |   file:
16 |     path: "/tmp/bioc_sync/rclone"
17 |     state: directory
18 |     mode: '0700'
19 | 
20 | - name: Write rclone config
21 |   copy:
22 |     content: "{{ lookup('env', 'RCLONE_CONF_CONTENTS') }}"
23 |     dest: "/tmp/bioc_sync/rclone/rclone.conf"
24 |     mode: '0600'
25 | 
26 | - name: Create paths file
27 |   template:
28 |     src: paths.j2
29 |     dest: /tmp/paths
30 |     mode: '0644'
31 | 
32 | - name: Run rsync
33 |   shell: |
34 |     rsync -e "ssh -i /tmp/bioc_sync/rsync-key.pem" -zrtlv bioc-rsync@master.bioconductor.org:{{ bioc_version }} ./
35 | 
36 | - name: Run rclone sync
37 |   environment:
38 |     RCLONE_CONFIG: "/tmp/bioc_sync/rclone/rclone.conf"
39 |   shell: |
40 |     cat /tmp/paths | xargs -i rclone copyto -vvv ./{}  osn:/bir190004-bucket01/archive.bioconductor.org/packages/{}
41 | 
42 | - name: Cleanup
43 |   file:
44 |     path: "/tmp/bioc_sync"
45 |     state: absent
46 | 


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/.github/workflows/sync-release.yml:
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 1 | name: Sync Bioconductor Release
 2 | 
 3 | on:
 4 |   workflow_dispatch:
 5 |     inputs:
 6 |       bioc_version:
 7 |         description: 'Bioconductor version to sync'
 8 |         required: true
 9 |         default: '3.19'
10 | 
11 | jobs:
12 |   sync:
13 |     runs-on: ubuntu-latest
14 |     steps:
15 |       - uses: actions/checkout@v4
16 | 
17 |       - name: Install Ansible
18 |         run: |
19 |           sudo apt update
20 |           sudo apt install -y ansible
21 | 
22 |       - name: Set up SSH key
23 |         run: |
24 |           mkdir -p ~/.ssh
25 |           echo "${{ secrets.VM_SSH_KEY }}" > ~/.ssh/vm_key
26 |           chmod 600 ~/.ssh/vm_key
27 |           echo "${{ secrets.RSYNC_PRIVATE_KEY }}" > rsync-key.pem
28 |           chmod 600 rsync-key.pem
29 | 
30 |       - name: Run Ansible playbook
31 |         env:
32 |           BIOC_VM_IP: ${{ secrets.BIOC_VM_IP }}
33 |           SSH_KEY_PATH: ~/.ssh/vm_key
34 |           RSYNC_PRIVATE_KEY: ${{ secrets.RSYNC_PRIVATE_KEY }}
35 |           RCLONE_CONF_CONTENTS: ${{ secrets.RCLONE_CONF_CONTENTS }}
36 |         run: |
37 |           ansible-playbook -i ansible/inventory/hosts.yml \
38 |             ansible/playbooks/sync_release.yml \
39 |             --extra-vars "biocver=${{ github.event.inputs.bioc_version }}"
40 | 


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