From 56802e61a7d63110ae624001e471692b08bf8b28 Mon Sep 17 00:00:00 2001
From: Dawa Ometto <d.l.a.ometto1@uu.nl>
Date: Tue, 1 Oct 2024 14:10:09 +0200
Subject: [PATCH] Use YAML config for job conf

---
 vars/galaxy_vars.yml | 69 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 68 insertions(+), 1 deletion(-)

diff --git a/vars/galaxy_vars.yml b/vars/galaxy_vars.yml
index 2ea7cc2..e6dd5f3 100644
--- a/vars/galaxy_vars.yml
+++ b/vars/galaxy_vars.yml
@@ -31,6 +31,67 @@ postgresql_objects_users:
 postgresql_objects_databases:
   - name: galaxy
     owner: galaxy
+galaxy_job_config:
+  runners:
+    local_runner:
+      load: galaxy.jobs.runners.local:LocalJobRunner
+      workers: 4
+    puslar_embedded:
+      load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+      workers: 4
+  handling:
+    assign: ['db-skip-locked']
+  execution:
+    default: "{{ _galaxy_use_interactive_tools | ternary('docker_dispatch', 'local_env') }}"
+    environments:
+      local_env:
+        runner: local_runner
+        tmp_dir: true
+      docker_interactive:
+        runner: "{{ _galaxy_jobs_pulsar_embedded | ternary('pulsar_embedded', 'local_runner') }}"
+        docker_enabled: true
+        docker_volumes: $defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro
+        docker_sudo: false
+        docker_net: bridge
+        docker_auto_rm: true
+        docker_set_user:
+        require_container: true
+        container_monitor_result: callback
+        env:
+          REQUESTS_CA_BUNDLE: /etc/ssl/certs/ca-certificates.crt
+      docker_dispatch:
+        runner: dynamic
+        type: docker_dispatch
+        docker_destination_id: docker_interactive
+        default_destination_id: local_env
+      singularity:
+        singularity_volumes: "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,{{ galaxy_data_dir }}:rw"
+        runner: local_runner
+        singularity_enabled: true
+        container_resolvers:
+          - type: cached_explicit_singularity
+            cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/explicit/"
+          - type: cached_mulled_singularity
+            cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/mulled/"
+          - type: mulled_singularity
+            auto_install: False
+            cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/mulled/"
+          - type: build_mulled_singularity
+            auto_install: False
+            cache_directory: "{{ galaxy_mutable_data_dir }}/cache/singularity/built/"
+        env:
+          # Ensuring a consistent collation environment is good for reproducibility.
+          - name: LC_ALL
+            value: C
+          # The cache directory holds the docker containers that get converted
+          - name: APPTAINER_CACHEDIR
+            value: /tmp/singularity
+          # Apptainer uses a temporary directory to build the squashfs filesystem
+          - name: APPTAINER_TMPDIR
+            value: /tmp
+  tools:
+    - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
+      environment: local_env
 galaxy_configuration:
   galaxy:
     use_remote_user: true
@@ -40,7 +101,7 @@ galaxy_configuration:
     remote_user_maildomain: "{{ _galaxy_remote_user_maildomain }}"
     database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
     file_path: "{{ galaxy_mutable_data_dir }}/datasets"
-    job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
+    job_config: "{{ galaxy_job_config }}"
     tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml"
     user_preferences_extra_conf_path: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
     interactivetools_enable: "{{ _galaxy_use_interactive_tools }}"
@@ -73,6 +134,12 @@ galaxy_configuration:
       pool: threads
       memory_limit: 2
       loglevel: DEBUG
+    handlers:
+      handler:
+        processes: 4
+        pools:
+          - job-handlers
+          - workflow-schedulers
     gx_it_proxy:
       enable: "{{ _galaxy_use_interactive_tools }}"
       port: "{{ gie_proxy_port }}"