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Add functionality and documentation for building Conda pacakges. #643

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merged 1 commit into from Feb 27, 2017
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Add functionality and documentation for building Conda pacakges. #643

merged 1 commit into from Feb 27, 2017

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jmchilton
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@jmchilton jmchilton commented Feb 24, 2017 •
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  • Add documentation that links out to external sources for building Conda recipes - recommending specific docs and a specific order.
  • Allow Planemo to work with locally built Conda packages using the --conda_use_local command.
  • Add an exercise to the documentation that requires building a package and the use of --conda_use_local. This uses a new project template that adds a tool targeting the package https://github.com/jmchilton/fleeqtk I forked from seqtk for this purpose.
  • Update galaxy-lib dependency for the required library functionality to use --conda_use_local.
  • Add test case that follows the example in the documentation targeting the fleeqtk package. It builds a fleeqk recipe, uses conda_install --conda_use_local on a tool that requires it, and finally runs planemo test to ensure that Galaxy properly uses the resulting package.

Fixes #620

@jmchilton jmchilton mentioned this pull request Feb 24, 2017
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@jmchilton jmchilton added this to the GCC 2017 milestone Feb 24, 2017
bgruening
bgruening approved these changes Feb 25, 2017
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Great stuff John - as usual!

tests/data/repos/conda_exercises_fleeqtk/fleeqtk_seq.xml
@@ -0,0 +1,102 @@
<tool id="fleeqtk_seq" name="Convert to FASTA (fleeqtk)" version="0.1.0">
<stdio>
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should we get rid of stdio here?

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Yeah - but this was based on the seqtk tutorial and tool_init. I have created an issue for this here #644. I'll get to this before say the GCC I think - but I want to do every variant of seqtk in the code base at once after that issue is addressed.

tests/data/repos/conda_exercises_fleeqtk/fleeqtk_seq.xml
<command><![CDATA[
fleeqtk seq
#if $settings.advanced == "advanced"
$settings.shift_quality
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I would like to see here indentations to make it more readable

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Yeah - good plan. I think I want to update the seqtk tools at the same time. I created an issue #645.

docs/_writing_dependencies_conda.rst Outdated
- `Contributing a recipe <https://bioconda.github.io/contribute-a-recipe.html>`__ (through "Write a Recipe")
- `Building Conda Package <https://conda.io/docs/building/bpp.html#>`__ in particular

- `Building conda packages with conda skeleton <https://conda.io/docs/build_tutorials/pkgs.html>`__
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Maybe highlight with a single sentence that skeletons are the usual way to create templates for scripting languages ... so that people don't start to write this by hand?

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Cool - I will rebase this with that advice - thanks!

@jmchilton jmchilton mentioned this pull request Feb 27, 2017
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@jmchilton
Add functionality and documentation for building Conda pacakges.
24764cd 
- Add documentation that links out to external sources for building Conda recipes - recommending specific docs and a specific order.
- Allow Planemo to work with locally built Conda packages using the ``--conda_use_local`` command.
- Add an exercise to the documentation that requires building a package and the use of ``--conda_use_local``. This uses a new project template that adds a tool targeting the package https://github.com/jmchilton/fleeqtk I forked from seqtk for this purpose.
- Update galaxy-lib dependency for the required library functionality to use ``--conda_use_local``.
- Add test case that follows the example in the documentation targeting the fleeqtk package. It builds a fleetqk recipe, uses conda_install --conda_use_local on a tool that requires it, and finally runs planemo test to ensure that Galaxy properly uses the resulting package.
@bgruening bgruening merged commit 96782cd into galaxyproject:master Feb 27, 2017
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Thanks John!

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