tool_defaults.yml

---
# ALL tags must be with dashes (-) instead of underscores (_)
global:
  default_inherits: default
tools:
  default:
    cores: 1
    mem: cores * 3.8
    gpus: 0
    env:
      GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
    params:
      metadata_strategy: 'extended'
      tmp_dir: true
      request_cpus: "{cores}"
      request_memory: "{mem}G"
      submit_request_gpus: "{gpus or 0}"
      docker_memory: "{mem}G"
      description: "{tool.id if not tool.id.count('/') == 5 else tool.id.split('/')[4]}"
    scheduling:
      reject:
        - offline
    rules:
      - if: user is not None
        execute: |
          training_roles = [r.name for r in user.all_roles() if not r.deleted and "training" in r.name]
          training_expr = " || ".join(['(GalaxyGroup == "%s")' % role for role in training_roles])
          training_labels = '"' + ", ".join(training_roles) + '"'
          entity.params['requirements'] = '(GalaxyGroup == "compute") || (%s)' % training_expr if training_expr else '(GalaxyGroup == "compute")'
          entity.params['+Group'] = training_labels
          entity.params['accounting_group_user'] = str(user.id)
      - id: remote_resources
        if: user is not None
        execute: |
          from tpv.core.entities import Tag, TagSetManager, TagType

          user_preferences = user.extra_preferences
          pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None")
          pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None

          if pulsar_tag:
              entity.tpv_tags = entity.tpv_tags.combine(
                  TagSetManager(tags=[pulsar_tag])
              )
      - id: cz-pulsar_alphafold
        if: |
          all((
              "cz-pulsar" in {tag.value for tag in entity.tpv_tags.tags},
              tool.id.startswith("toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold"),
              helpers.tool_version_gte(tool, '2.3.1'),
          ))
        gpus: 1

    rank: |
      final_destinations = helpers.weighted_random_sampling(candidate_destinations)
      final_destinations