Welcome to Planemo’s documentation!

Contents:

• Quick Start
  • Obtaining
  • Basics - Galaxy
  • Basics - Common Workflow Language
  • Tool Shed
  • Conda
  • Docker and Containers
• Installation
  • pip
  • Conda (Experimental)
• Configuration
• Virtual Appliance
  • Quick Links
  • The Setup
  • Launching the Appliance
  • Building the Appliance
• Building Galaxy Tools
  • ...using Planemo
  • ...using a Planemo Virtual Appliance
  • Advanced Tool Development Topics
  • How do I... (Reference FAQ)
• Building Common Workflow Language Tools
  • ...using Planemo
  • ...using a Planemo Virtual Appliance
  • Advanced Tool Development Topics
• Publishing to the Tool Shed
  • Configuring a Shed Account
  • Creating a Repository
  • Updating a Repository
  • Advanced Usage
• Test Format
  • job
  • outputs
  • Engines for Testing
  • Galaxy Testing Template
• Best Practices for Creating Galaxy Tools
  • Why you might read this
  • Definitions
  • Tools and Tool Development
  • Packages
  • Repository Layout
  • .shed.yml
  • Repository Management
• Best Practices for Maintaining Galaxy Workflows
  • Workflow Structure
  • Tests
  • Publishing
• Running Galaxy workflows
  • The Basics
  • Workflow execution against an external Galaxy
  • Generating the job file
  • Using workflow and dataset IDs
  • Using aliases
  • Checking invocations
  • Profile configuration files
  • Rerunning failed jobs
• Automating Galaxy Workflows
• Autoupdating tools
  • Formatting tools
  • Updating workflows
  • Implementing an autoupdate CI job
• Commands
  • autoupdate command
  • ci_find_repos command
  • ci_find_tools command
  • clone command
  • conda_build command
  • conda_env command
  • conda_init command
  • conda_install command
  • conda_lint command
  • conda_search command
  • config_init command
  • container_register command
  • create_alias command
  • database_create command
  • database_delete command
  • database_list command
  • delete_alias command
  • docker_build command
  • docker_shell command
  • dockstore_init command
  • docs command
  • lint command
  • list_alias command
  • list_invocations command
  • list_repos command
  • merge_test_reports command
  • mull command
  • mulled_init command
  • normalize command
  • open command
  • profile_create command
  • profile_delete command
  • profile_list command
  • project_init command
  • pull_request command
  • run command
  • serve command
  • share_test command
  • shed_build command
  • shed_create command
  • shed_diff command
  • shed_init command
  • shed_lint command
  • shed_serve command
  • shed_test command
  • shed_update command
  • shed_upload command
  • syntax command
  • test command
  • test_reports command
  • tool_init command
  • training_fill_data_library command
  • training_generate_from_wf command
  • training_init command
  • workflow_convert command
  • workflow_edit command
  • workflow_job_init command
  • workflow_lint command
  • workflow_test_init command
  • workflow_upload command
• Galaxy Tool Framework Changes
  • John Chilton
• Planemo Project Code of Conduct
• Contributing
  • Types of Contributions
  • Get Started!
  • Pull Request Guidelines
  • Tips
• Project Governance
  • Benevolent Dictator for Now (BDFN)
  • Committers
• Release Checklist
• History
  • 0.75.0.dev0
  • 0.74.9 (2021-11-03)
  • 0.74.8 (2021-10-10)
  • 0.74.7 (2021-09-21)
  • 0.74.6 (2021-07-23)
  • 0.74.5 (2021-06-25)
  • 0.74.4 (2021-06-01)
  • 0.74.3 (2021-02-25)
  • 0.74.2 (2021-02-21)
  • 0.74.1 (2021-01-03)
  • 0.74.0 (2020-12-30)
  • 0.73.0 (2020-12-28)
  • 0.72.0 (2020-08-04)
  • 0.71.0 (2020-08-03)
  • 0.70.0 (2020-01-29)
  • 0.62.1 (2019-10-14)
  • 0.62.0 (2019-10-11)
  • 0.61.0 (2019-07-08)
  • 0.60.0 (2019-05-31)
  • 0.59.0 (2019-05-09)
  • 0.58.2 (2019-03-01)
  • 0.58.1 (2019-01-03)
  • 0.58.0 (2019-01-01)
  • 0.57.1 (2018-11-23)
  • 0.57.0 (2018-11-19)
  • 0.56.0 (2018-10-30)
  • 0.55.0 (2018-09-12)
  • 0.54.0 (2018-06-06)
  • 0.53.0 (2018-05-22)
  • 0.52.0 (2018-05-20)
  • 0.51.0 (2018-05-19)
  • 0.50.1 (2018-05-11)
  • 0.50.0 (2018-05-10)
  • 0.49.2 (2018-05-09)
  • 0.49.1 (2018-05-06)
  • 0.49.0 (2018-05-06)
  • 0.48.0 (2018-02-28)
  • 0.47.0 (2017-11-18)
  • 0.46.1 (2017-09-26)
  • 0.46.0 (2017-09-15)
  • 0.45.0 (2017-09-06)
  • 0.44.0 (2017-06-22)
  • 0.43.0 (2017-06-22)
  • 0.42.1 (2017-06-16)
  • 0.42.0 (2017-06-15)
  • 0.41.0 (2017-06-05)
  • 0.40.1 (2017-05-03)
  • 0.40.0 (2017-03-16)
  • 0.39.0 (2017-03-15)
  • 0.38.1 (2017-02-06)
  • 0.38.0 (2017-02-06)
  • 0.37.0 (2017-01-25)
  • 0.36.1 (2016-12-12)
  • 0.36.0 (2016-12-11)
  • 0.35.0 (2016-11-14)
  • 0.34.1 (2016-10-12)
  • 0.34.0 (2016-10-05)
  • 0.33.2 (2016-09-28)
  • 0.33.1 (2016-09-28)
  • 0.33.0 (2016-09-23)
  • 0.32.0 (2016-09-16)
  • 0.31.0 (2016-09-06)
  • 0.30.2 (2016-09-01)
  • 0.30.1 (2016-09-01)
  • 0.30.0 (2016-09-01)
  • 0.29.1 (2016-08-19)
  • 0.29.0 (2016-08-19)
  • 0.28.0 (2016-08-17)
  • 0.27.0 (2016-06-22)
  • 0.26.0 (2016-05-20)
  • 0.25.1 (2016-05-11)
  • 0.25.0 (2016-05-11)
  • 0.24.2 (2016-04-25)
  • 0.24.1 (2016-04-08)
  • 0.24.0 (2016-03-29)
  • 0.23.0 (2016-02-15)
  • 0.22.2 (2016-01-14)
  • 0.22.1 (2016-01-14)
  • 0.22.0 (2016-01-13)
  • 0.21.1 (2015-11-29)
  • 0.21.0 (2015-11-29)
  • 0.20.0 (2015-11-11)
  • 0.19.0 (2015-11-03)
  • 0.18.1 (2015-10-22)
  • 0.18.0 (2015-10-20)
  • 0.17.0 (2015-10-19)
  • 0.16.0 (2015-10-07)
  • 0.15.0 (2015-10-01)
  • 0.14.0 (2015-08-06)
  • 0.13.2 (2015-07-06)
  • 0.13.1 (2015-07-01)
  • 0.13.0 (2015-06-28)
  • 0.12.2 (2015-05-23)
  • 0.12.1 (2015-05-21)
  • 0.12.0 (2015-05-21)
  • 0.11.1 (2015-05-12)
  • 0.11.0 (2015-05-12)
  • 0.10.0 (2015-05-06)
  • 0.9.0 (2015-05-03)
  • 0.8.4 (2015-04-30)
  • 0.8.3 (2015-04-29)
  • 0.8.2 (2015-04-29)
  • 0.8.1 (2015-04-28)
  • 0.8.0 (2015-04-27)
  • 0.7.0 (2015-04-13)
  • 0.6.0 (2015-03-16)
  • 0.5.0 (2015-02-22)
  • 0.4.2 (2015-02-21)
  • 0.4.1 (2015-02-16)
  • 0.4.0 (2015-02-16)
  • 0.3.1 (2015-02-15)
  • 0.3.0 (2015-02-13)
  • 0.2.0 (2015-01-13)
  • 0.1.0 (2014-12-16)
  • 0.0.1 (2014-10-04)

Indices and tables

• Index
• Module Index
• Search Page