martenson / usegalaxy-tools

usegalaxy.* common tools

usegalaxy.* tools

WORK IN PROGRESS

Setup

• yaml files are manually curated
• yaml.lock files are automatically generated
• Only IUC tools are automatically updated with the latest version each week
• Use the provided requirements.txt to install dependences needed for the make targets

Updating an Existing Tool

1. Edit the .yaml.lock file to add the latest/specific changeset revision for the tool. You can use python scripts/update-tool.py --owner <repo-owner> --name <repo-name> <file.yaml.lock> in order to do this if you just want to add the latest revision.
2. Open a pull request

Requesting a New Tool

• If you just want the latest version:
  • Edit the .yaml file to add name/owner/section
• If you want a specific version:
  • Edit the .yaml file to add name/owner/section
  • Run make fix
  • Edit the .yaml.lock to correct the version number.
• Open a pull request

Tips

Use make TOOLSET=<toolset_dir> <target> to limit a make action to a specific toolset subdirectory, e.g.:

$ make TOOLSET=usegalaxy.org lint
find ./usegalaxy.org -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 python scripts/fix-lockfile.py
find ./usegalaxy.org -name '*.yml' | grep '^\./[^/]*/' | xargs -n 1 -P 8 -I{} pykwalify -d '{}' -s .schema.yml
 INFO - validation.valid
 INFO - validation.valid
 ...