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galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
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shed_tools install fails with `KeyError: 'tool_shed_url'` #124

Closed pcm32 closed 5 years ago

pcm32 commented 5 years ago

After installing from master:

pip install https://github.com/galaxyproject/ephemeris/archive/master.zip

calling:

shed-tools install -t tools.yaml -g <instance> -a <key>
....
lib/python2.7/site-packages/ephemeris/get_tool_list_from_galaxy.py", line 186, in merge_repository_changeset_revisions
    repo_key = repo_key_template.format(**repo)
KeyError: 'tool_shed_url'

The yaml file records look like this:

tools:
- name: cutadapt
  owner: lparsons
  tool_panel_section_label: RNA-Seq
  tool_shed_url: "https://toolshed.g2.bx.psu.edu/"
  revisions:
  - 660cffd8d92a
- name: data_manager_fetch_genome_dbkeys_all_fasta
  owner: devteam
  tool_panel_section_label: RNA-Seq
  tool_shed_url: "https://toolshed.g2.bx.psu.edu/"
  revisions:
  - b1bc53e9bbc5

This works when using a virtualenv with ephemeris installed through pip install ephemeris.