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planemo shed_lint and tool_dependency_definition #156

peterjc opened this Issue Apr 30, 2015 · 2 comments


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peterjc commented Apr 30, 2015

For a tool dependency definition there should be only two files present, .shed.yml and tool_dependencies.xml (since the Tool Shed insists on just the tool_dependencies.xml being uploaded, not even allowing a README file).

$ more galaxy_blast/dependencies/package_blast_plus_2_2_30/.shed.yml
name: package_blast_plus_2_2_30
owner: iuc
description: NCBI BLAST+ 2.2.30 (binaries only) 
long_description: |
  This Tool Shed package is intended to be used as a dependency of the Galaxy wrappers
  for NCBI BLAST+ and any other tools which call the BLAST+ binaries internally.

  Development is hosted on GitHub which can
  be used for reporting any issues.
- Sequence Analysis
type: tool_dependency_definition
$ planemo shed_lint galaxy_blast/dependencies/package_blast_plus_2_2_30
Linting repository /mnt/galaxy/repositories/galaxy_blast/dependencies/package_blast_plus_2_2_30
Applying linter dependencies... CHECK
.. INFO: tool_dependencies.xml found and appears to be valid XML
Applying linter itory_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter e... CHECK
.. INFO: No README found skipping.

Having looked at the .shed.yml and noticed type: tool_dependency_definition, rather than looking at any repository_dependencies.xml this should be checking there isn't such a file.

Having a README file would be harmless (not used by the ToolShed, but might be useful for humans, and would be shown on GitHub/Bitbucket etc).


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jmchilton commented Apr 30, 2015

Extra files are no longer a problem - planemo shed_upload will just not "realize" invalid files for the given repository type - so you can have a README, CONTRIBUTING, LICENSE, etc... on github - they just won't be published to the tool shed. That said - I think it planemo shed_lint should definitely verify a package_ repository has a tool_dependencies.xml file and suite_ repository has a repository_dependencies.xml file and perhaps even that they don't have the opposite.


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peterjc commented Apr 30, 2015

+1 on verifying there is a tool_dependencies.xml for package repositories.

@peterjc peterjc referenced this issue Apr 30, 2015


Implement shed_lint. #107

10 of 11 tasks complete

@jmchilton jmchilton closed this in 76fed9b May 6, 2015

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