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fix- pip ignores bioconda_scripts #614

merged 1 commit into from Jan 9, 2017


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nturaga commented Dec 28, 2016

This should fix this issue, #493.

(planemo_env) ~/test❯❯❯ planemo
Problem loading command bioc_conda_recipe_init, exception No module named bioconda_scripts
Problem loading command bioc_tool_init, exception No module named bioconda_scripts
Usage: planemo [OPTIONS] COMMAND [ARGS]...

  A command-line toolkit for building tools and workflows for Galaxy.

  Check out the full documentation for Planemo online or open with ``planemo docs``.

  --version         Show the version and exit.
  -v, --verbose     Enables verbose mode.
  --config TEXT     Planemo configuration YAML file.
  --directory TEXT  Workspace for planemo.
  --help            Show this message and exit.

  brew                   Install tool requirements using brew.
  brew_env               List commands to inject brew dependencies.
  brew_init              Download linuxbrew install & run it in ruby.
  ci_find_repos          Find all shed repositories in one or more...
  ci_find_tools          Find all tools in one or more directories.
  clone                  Short-cut to quickly clone, fork, and branch...
  conda_env              Activate a conda environment for tool.
  conda_init             Download and install conda.
  conda_install          Install conda packages for tool requirements.
  conda_lint             Check conda recipe for common issues.
  config_init            Initialise global configuration for Planemo.
  create_gist            Upload file to GitHub as a sharable gist.

@nturaga nturaga added the bug label Dec 28, 2016

@nturaga nturaga self-assigned this Dec 28, 2016

@nturaga nturaga requested a review from jmchilton Dec 28, 2016


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malloryfreeberg commented Jan 9, 2017

@jmchilton can you please merge this PR if everything looks good? We need this to be fixed so that one of the reviewers of the F1000 publication can successfully install planemo with the new R/Bioconductor wrapping commands (bioc_tool_init and bioc_conda_recipe_init). Thanks!

@bgruening bgruening merged commit f08375a into galaxyproject:master Jan 9, 2017

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bgruening commented Jan 9, 2017

If you need a new release you need to wait for John. But pip install from github should work as well!


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malloryfreeberg commented Jan 9, 2017

Thanks @bgruening !

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