wm75 / usegalaxy-tools

usegalaxy.* common tools

usegalaxy.* tools

WORK IN PROGRESS

Using these tools

Add the following dependency resolver:

<conda prefix="/cvmfs/sandbox.galaxyproject.org/dependencies/conda" auto_install="False" auto_init="False" />

preferably above your existing conda dependency resolver (you will need to set conda_auto_install: false in your galaxy.yml).

And add the new shed tool conf:

tool_config_file: ...,/cvmfs/sandbox.galaxyproject.org/config/shed_tool_conf.xml

In your destination you should set:

<param id="singularity_enabled">true</param>
<param id="singularity_volumes">$defaults</param>

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 (or make fix-no-deps for non-Conda toolsets like cloud)
  • 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
 ...