Configuring Galaxy

Simple configuration

  1. First install the TotalPerspectiveVortex into your Galaxy virtual environment.

cd <galaxy_home>
source .venv/bin/activate
pip install --upgrade total-perspective-vortex

  1. Edit your job_conf.yml in the <galaxy_home>/config folder and add the highlighted sections to it.

    You can refer to a local file for the tpv_config_files setting, or alternatively, provider a link to a remote url.

 1runners:
 2  local:
 3    load: galaxy.jobs.runners.local:LocalJobRunner
 4    workers: 4
 5  drmaa:
 6    load: galaxy.jobs.runners.drmaa:DRMAAJobRunner
 7  k8s:
 8    load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
 9
10handling:
11  assign:
12    - db-skip-locked
13
14execution:
15  default: tpv_dispatcher
16  environments:
17    tpv_dispatcher:
18      runner: dynamic
19      type: python
20      function: map_tool_to_destination
21      rules_module: tpv.rules
22      tpv_config_files:
23        - https://github.com/galaxyproject/total-perspective-vortex/raw/main/tpv/tests/fixtures/mapping-rules.yml
24        - config/tpv_rules_local.yml
25    local:
26      runner: local
27    k8s_environment:
28      runner: k8s
29      docker_enabled: true

  1. Add your own custom rules to your local tpv_config_file, following instructions in the next section.

Combining multiple remote and local configs

TPV allows rules to be loaded from remote or local sources.

1 tpv_dispatcher:
2  runner: dynamic
3  type: python
4  function: map_tool_to_destination
5  rules_module: tpv.rules
6  tpv_config_files:
7    - https://usegalaxy.org/shared_rules.yml
8    - config/tpv_rules_australia.yml

The config files listed first are overridden by config files listed later. The normal rules of inheritance apply. This allows a central database of common rules to be maintained, with individual, site-specific overrides.