updates TPV script in TPV role and GCZ specific TPV config

files/usegalaxy.cz/tpv_rules_local.yml.j2

@@ -0,0 +1,70 @@
+global:
+  default_inherits: default
+destinations:
+  tpv_pulsar_rosettafold:
+    inherits: tpv_pulsar
+    runner: pulsar_tpv_runner
+    params:
+      singularity_enabled: false
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+    scheduling:
+      require:
+        - rosettafold
+  tpv_pulsar_rosettafold_sing:
+    inherits: tpv_pulsar_rosettafold
+    container_resolvers:
+    -   type: explicit_singularity
+    -   cache_directory: /cvmfs/singularity.metacentrum.cz/RoseTTAFold2/
+        type: cached_mulled_singularity
+    params:
+      singularity_enabled: true
+      singularity_run_extra_arguments: '--nv --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR'
+      singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights'
+      singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif"
+    scheduling:
+      require:
+        - singularity
+  tpv_pulsar_alphafold:
+    inherits: tpv_pulsar
+    max_accepted_gpus: 1
+    max_gpus: 1
+    runner: pulsar_tpv_runner
+    params:
+      singularity_run_extra_arguments: '--nv'
+      singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro'
+      submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}"
+    scheduling:
+      require:
+        - alphafold
+tools:
+  testing_rosettafold2:
+    cores: 8
+    mem: 64
+    gpus: 1
+    context:
+      walltime: 24
+      scratch: 25
+      gpu_mem: 16
+    scheduling:
+      require:
+        - rosettafold
+  rosettafold2:
+    inherits: testing_rosettafold2
+    scheduling:
+      require:
+        - singularity
+  toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*:
+    cores: 8
+    mem: 120
+    gpus: 1
+    context:
+      walltime: 24
+      scratch: 100
+      gpu_mem: 16
+    env:
+      MPLCONFIGDIR: "$SCRATCHDIR"
+      ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db"
+      ALPHAFOLD_USE_GPU: True
+    scheduling:
+      require:
+        - alphafold

host_vars/usegalaxy.cz/vars.yml

@@ -28,8 +28,6 @@ pulsar:
 galaxy_config_files:
   - src: files/galaxy/themes.yml
     dest: "{{ galaxy_config.galaxy.themes_config_file }}"
-  - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml', 'files/galaxy/config/tpv_rules_local.yml']) }}"
-    dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml"
   - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}"
     dest: "{{ galaxy_config_dir }}/tool_conf.xml"
   - src: files/galaxy/config/oidc_config.xml
@@ -41,6 +39,22 @@ galaxy_config_files:
   - src: files/{{ inventory_hostname }}/user_preferences_extra_conf.yml
     dest: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
 
+galaxy_config_templates:
+  - src: "templates/{{ inventory_hostname }}/config/object_store_conf.xml.j2"
+    dest: "{{ galaxy_config.galaxy.object_store_config_file }}"
+  - src: "templates/{{ inventory_hostname }}/config/local_tool_conf.xml.j2"
+    dest: "{{ galaxy_config_dir }}/local_tool_conf.xml"
+  - src: templates/galaxy/config/tpv_rules_meta.yml.j2
+    dest: "{{ tpv_mutable_dir }}/tpv_rules_meta.yml"
+  - src: "templates/galaxy/config/vault_conf.yml.j2"
+    dest: "{{ galaxy_config_dir }}/vault_conf.yml"
+  - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/auth_conf.xml.j2', 'templates/galaxy/config/auth_conf.xml.j2']) }}"
+    dest: "{{ galaxy_config.galaxy.auth_config_file }}"
+  - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/file_source_templates.yml.j2', 'templates/galaxy/config/file_source_templates.yml.j2']) }}"
+    dest: "{{ galaxy_config_dir }}/file_source_templates.yml"
+  - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml.j2', 'files/galaxy/config/tpv_rules_local.yml']) }}"
+    dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml"
+
 galaxy_local_tools:
   - testing.xml
   - testing_pbs.xml

roles/usegalaxy_eu.tpv_auto_lint/.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+---
+name: Ansible-lint
+
+'on':
+  push:
+
+defaults:
+  run:
+    working-directory: 'ansible-tpv-lint'
+
+jobs:
+  ansible-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'ansible-tpv-lint'
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install ansible ansible-lint
+      - name: Lint playbook
+        run: |
+          if ! ansible-lint; then
+            exit 1
+          fi

roles/usegalaxy_eu.tpv_auto_lint/.github/workflows/import.yml

@@ -0,0 +1,38 @@
+---
+# This workflow requires a GALAXY_API_KEY secret present in the GitHub
+# repository or organization.
+#
+# See: https://github.com/marketplace/actions/publish-ansible-role-to-galaxy
+# See: https://github.com/ansible/galaxy/issues/46
+
+name: "Ansible-Galaxy import"
+
+on:
+  workflow_dispatch:
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the codebase.
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+
+      - name: Install Ansible.
+        run: pip3 install ansible-base
+
+      # We have to do this step as GHA prevents triggering it's own actions, to
+      # prevent runaway loops.
+      - name: Trigger a new import on Galaxy.
+        run: |
+          org=$(echo ${{ github.repository }} | cut -d/ -f1)
+          repo=$(echo ${{ github.repository }} | cut -d/ -f2)
+          key=${{ secrets.ANSIBLE_GALAXY_API_KEY }}
+          ansible-galaxy role import --api-key $key $org $repo --branch main

roles/usegalaxy_eu.tpv_auto_lint/.github/workflows/release.yml

@@ -0,0 +1,32 @@
+---
+# This workflow requires a GALAXY_API_KEY secret present in the GitHub
+# repository or organization.
+#
+# See: https://github.com/marketplace/actions/publish-ansible-role-to-galaxy
+# See: https://github.com/ansible/galaxy/issues/46
+
+name: Release
+
+'on':
+  push:
+    tags:
+      - '*'
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the codebase.
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install Ansible.
+        run: pip3 install ansible-base
+
+      - name: Trigger a new import on Galaxy.
+        run: ansible-galaxy role import --api-key ${{ secrets.ANSIBLE_GALAXY_API_KEY }} $(echo ${{ github.repository }} | cut -d/ -f1) $(echo ${{ github.repository }} | cut -d/ -f2) --branch main --role-name tpv_auto_lint

roles/usegalaxy_eu.tpv_auto_lint/.github/workflows/slugger.yml

@@ -0,0 +1,72 @@
+---
+# This workflow requires a GALAXY_API_KEY secret present in the GitHub
+# repository or organization.
+#
+# See: https://github.com/marketplace/actions/publish-ansible-role-to-galaxy
+# See: https://github.com/ansible/galaxy/issues/46
+#
+# Note on the file name:
+#   Reminding me (@hexylena) to make a release of a role was the last thing
+#   @Slugger70 asked me our group chat. I'd forgotten to do it and he was
+#   waiting on me for it, well, here's to you mate, none of us can forget to
+#   make a point release again.
+
+name: "Automatic Regular Releases"
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * 1'
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the codebase.
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+
+      - name: Install Ansible.
+        run: pip3 install ansible-base
+
+      - name: Check for changes
+        run: |
+          LATEST_TAG=$(git describe --tags --abbrev=0)
+          echo "The last released tag was ${LATEST_TAG}"
+          CHANGES=$(git diff ${LATEST_TAG} --name-only | wc -l)
+          echo "Found ${CHANGES} changed files"
+          git diff ${LATEST_TAG} --name-only
+          echo "changed_files=${CHANGES}" >> $GITHUB_ENV
+
+      - name: Create a new git tag
+        run: |
+          LATEST_TAG=$(git describe --tags --abbrev=0)
+          major_minor=$(echo "$LATEST_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\1/')
+          patch=$(echo "$LATEST_TAG" | sed 's/\(.*\..*\.\)\(.*\)/\2/')
+          newpatch=$(echo "$patch + 1" | bc)
+          NEW_TAG="${major_minor}${newpatch}"
+          echo "$LATEST_TAG -> $NEW_TAG"
+
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git tag "$NEW_TAG"
+          git push --tags
+          echo "Creating new tag $NEW_TAG" >> $GITHUB_STEP_SUMMARY
+        if: env.changed_files > 0
+
+      # We have to do this step as GHA prevents triggering it's own actions, to
+      # prevent runaway loops.
+      - name: Trigger a new import on Galaxy.
+        run: |
+          org=$(echo ${{ github.repository }} | cut -d/ -f1)
+          repo=$(echo ${{ github.repository }} | cut -d/ -f2)
+          key=${{ secrets.ANSIBLE_GALAXY_API_KEY }}
+          ansible-galaxy role import --api-key $key $org $repo --branch main
+        if: env.changed_files > 0

roles/usegalaxy_eu.tpv_auto_lint/README.md

@@ -0,0 +1,17 @@
+# TPV Auto Lint
+Ansible role to create a script that automatically lints all YAML files in the `tpv_mutable_dir` and checks for their existence in Galaxy's `job_conf.yml`. If both applies, it copies the file to the TPV rules directory, updating existing files.
+This leads to a automatic reload, if Galaxy watches this directory.
+With this script, TPV in Galaxy's job handlers can't break anymore. Which would otherwise lead to mostly undetected destination mapping failures.
+
+## Requirements
+ - Ansible >= 2.11  
+ - [galaxyproject.galaxy](https://galaxy.ansible.com/galaxyproject/galaxy) for TPV and the `galaxy_*` vars
+
+## Role Variables
+See [defaults/main](./default/main.yml) or galaxy's [default/main](https://github.com/galaxyproject/ansible-galaxy/blob/main/defaults/main.yml)
+## Playbook Example
+Include role in your Galaxyserver Playbook **after** the galaxyproject.galaxy role (the dirs have to exist already)
+## License
+GPLv3
+## Author Information
+[Galaxy Europe](https://galaxyproject.org/eu/)

roles/usegalaxy_eu.tpv_auto_lint/defaults/main.yml

@@ -0,0 +1,6 @@
+tpv_mutable_dir: "{{ galaxy_mutable_data_dir }}/total_perspective_vortex"
+tpv_config_dir_name: TPV_DO_NOT_TOUCH
+tpv_config_dir: "{{ galaxy_config_dir }}/{{ tpv_config_dir_name }}"
+galaxy_job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
+tpv_privsep: false
+tpv_env_name: tpv_dispatcher

roles/usegalaxy_eu.tpv_auto_lint/meta/.galaxy_install_info

@@ -0,0 +1,2 @@
+install_date: 'Fri 23 May 2025 09:39:42 PM '
+version: 0.4.4

roles/usegalaxy_eu.tpv_auto_lint/meta/main.yml

@@ -0,0 +1,16 @@
+galaxy_info:
+  author: Mira Kuntz
+  company: Galaxy Europe
+  namespace: usegalaxy_eu
+  role_name: tpv_auto_lint
+  description: Script that lints TPV rule files and checks if they exist in \
+   Galaxy's job_conf.yml before copying them to the TPC rules folder
+  license: GPL-3.0
+  min_ansible_version: "2.1"
+  galaxy_tags:
+    - galaxyproject
+  platforms:
+    - name: EL
+      versions:
+        - "8"
+        - "9"

roles/usegalaxy_eu.tpv_auto_lint/requirements.txt

@@ -0,0 +1,2 @@
+ansible-core
+ansible-lint

roles/usegalaxy_eu.tpv_auto_lint/tasks/main.yml

@@ -0,0 +1,18 @@
+---
+- name: Create TPV mutable dir
+  ansible.builtin.file:
+    state: directory
+    path: "{{ tpv_mutable_dir }}"
+    mode: 0755
+
+- name: Copy TPV lint-and-copy-script
+  ansible.builtin.template:
+    src: tpv-lint-and-copy.sh.j2
+    dest: "{{ tpv_mutable_dir }}/tpv-lint-and-copy.sh"
+    owner: root
+    group: root
+    mode: 0750
+
+- name: Execute TPV lint-and-copy-script
+  ansible.builtin.command:
+    cmd: "{{ tpv_mutable_dir }}/tpv-lint-and-copy.sh"

roles/usegalaxy_eu.tpv_auto_lint/templates/tpv-lint-and-copy.sh.j2

@@ -0,0 +1,37 @@
+#!/bin/bash
+# Script that copies files to TPV config dir, only if linting is successful
+
+PYTHONPATH="{{ galaxy_root }}/server/lib"
+VENV="{{ galaxy_venv_dir }}"
+TPV_MUTABLE_DIR="{{ tpv_mutable_dir }}"
+TPV_DIR="{{ tpv_config_dir }}"
+TPV_DIR_NAME="{{ tpv_config_dir_name }}"
+JOB_CONFIG_FILE="{{ galaxy_job_config_file }}"
+TPV_ENV_NAME="{{ tpv_env_name }}"
+
+echo "Installing TPV version 3.1.3 and yq"
+$VENV/bin/pip install total-perspective-vortex==3.1.3 yq
+echo "Activating the Galaxy VENV"
+. $VENV/bin/activate
+
+LOCAL_TPV_CONFIGS="$(yq -c '.galaxy.job_config.execution.environments.'${TPV_ENV_NAME}'.tpv_config_files[]' $JOB_CONFIG_FILE | grep -v '^\"http' | xargs basename -a | xargs -I {} echo \"${TPV_MUTABLE_DIR}/{}\" | xargs)"
+echo "Found the following local TPV configs: $LOCAL_TPV_CONFIGS"
+
+if PYTHONPATH=$PYTHONPATH tpv lint $LOCAL_TPV_CONFIGS; then
+        echo "lint successful, checking job configuration for file(s): $LOCAL_TPV_CONFIGS ..."
+	for f in $LOCAL_TPV_CONFIGS; do
+        	FNAME=$(basename "$f")
+                if grep -q "$TPV_DIR_NAME/$FNAME" "$JOB_CONFIG_FILE"; then
+                        echo "$FNAME is present in job configuration, copying..."
+                        [[ $(type -t cp) == "alias" ]] && unalias cp
+                        cp -bu "$f" "$TPV_DIR/$FNAME" {% if tpv_privsep %}&& chown root:{{ __galaxy_user_group }} "$TPV_DIR/$FNAME" {% endif %}
+
+                else
+                        echo "$FNAME is not present in job configuration, exiting..."
+                        exit 3 && true
+                fi
+	done
+else
+        echo "lint failed, file(s): $LOCAL_TPV_CONFIGS - not copied"
+        exit 3 && true
+fi