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Add functionality and documentation for building Conda pacakges. #643
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Great stuff John - as usual!
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<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.
<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
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- `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 | ||
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- `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!
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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 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.
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Thanks John! |
--conda_use_local
command.--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.--conda_use_local
.Fixes #620