galaxy.yml

@@ -11,7 +11,13 @@
     - git:
         repo: 'https://github.com/usegalaxy-eu/libraries-training-repo'
         dest: /libraries/
+  post_tasks:
+    - name: Install slurm-drmaa
+      package:
+        name: slurm-drmaa1
   roles:
+    - galaxyproject.repos
+    - galaxyproject.slurm
     - galaxyproject.postgresql
     - role: natefoo.postgresql_objects
       become: true

group_vars/all.yml

@@ -2,3 +2,13 @@
 cvmfs_role: client
 galaxy_cvmfs_repos_enabled: config-repo
 cvmfs_quota_limit: 500
+
+# Galaxy vars that will be reused by Pulsar
+galaxy_job_metrics_plugins:
+  - type: core
+  - type: cpuinfo
+  - type: meminfo
+  - type: uname
+  - type: env
+  - type: cgroup
+  - type: hostname

group_vars/galaxyservers.yml

@@ -101,6 +101,7 @@ galaxy_config_templates:
 
 # systemd
 galaxy_manage_systemd: yes
+galaxy_systemd_env: [DRMAA_LIBRARY_PATH="/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"]
 
 # Certbot
 certbot_auto_renew_hour: "{{ 23 |random(seed=inventory_hostname)  }}"
@@ -137,3 +138,13 @@ golang_gopath: '/opt/workspace-go'
 # Singularity target version
 singularity_version: "3.7.4"
 singularity_go_path: "{{ golang_install_dir }}"
+
+# Slurm
+slurm_roles: ['controller', 'exec'] # Which roles should the machine play? exec are execution hosts.
+slurm_nodes:
+- name: localhost # Name of our host
+  CPUs: 2         # Here you would need to figure out how many cores your machine has. For this training we will use 2 but in real life, look at `htop` or similar.
+slurm_config:
+  SlurmdParameters: config_overrides   # Ignore errors if the host actually has cores != 2
+  SelectType: select/cons_res
+  SelectTypeParameters: CR_CPU_Memory  # Allocate individual cores/memory instead of entire node

requirements.yml

@@ -18,3 +18,7 @@
   version: 2.6.3
 - src: galaxyproject.cvmfs
   version: 0.2.13
+- src: galaxyproject.repos
+  version: 0.0.2
+- src: galaxyproject.slurm
+  version: 0.1.3

templates/galaxy/config/job_conf.xml.j2

@@ -1,9 +1,16 @@
 <job_conf>
     <plugins workers="4">
         <plugin id="local_plugin" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
+        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner"/>
     </plugins>
-    <destinations default="singularity">
+    <destinations default="slurm">
         <destination id="local_destination" runner="local_plugin"/>
+        <destination id="slurm" runner="slurm">
+            <param id="singularity_enabled">true</param>
+            <env id="LC_ALL">C</env>
+            <env id="SINGULARITY_CACHEDIR">/tmp/singularity</env>
+            <env id="SINGULARITY_TMPDIR">/tmp</env>
+        </destination>
         <destination id="singularity" runner="local_plugin">
             <param id="singularity_enabled">true</param>
             <!-- Ensuring a consistent collation environment is good for reproducibility. -->