Configuring Galaxy
Simple configuration
First install TPV into your Galaxy virtual environment.
TPV is a conditional dependency of Galaxy since Galaxy 22.05. If TPV is enabled in your Galaxy job configuration, it will automatically be installed in the Galaxy virtualenv. Otherwise, or if you wish to upgrade to a newer version of TPV, you can use the process below to install manually:
cd <galaxy_home> source .venv/bin/activate pip install --upgrade total-perspective-vortex
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
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.
1tpv_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.