Configuring Galaxy
Simple configuration
First install the TotalPerspectiveVortex into your Galaxy virtual environment.
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.
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.