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add code for snakemake lesson #16

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Merged
merged 4 commits into from
Dec 17, 2019

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psteinb
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@psteinb psteinb commented Dec 10, 2019

Up until here, the code examples to do the snakemake parts are hidden in a versioned .tar.gz/.zip file inside files. This PR exposes this code in order to make it more testable. In this manor, the snakemake code can later be integrated with CI tools like travis, appveyor and others.

@psteinb psteinb removed the request for review from andrewsanchez December 13, 2019 15:29
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tkphd commented Dec 16, 2019

Is there a reason to retain the binary tar.gz files?

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psteinb commented Dec 16, 2019

well, that is possibly due to my ignorance. The binary files are retained in order to be able to download them later. If there is a way to make the tar.gz/zip files an artifact during a CI build, which can then be part of a release process. We could have the website point to that artifact online. Ideas?

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tkphd commented Dec 16, 2019

Ah-ha, I see: snakemake-lesson.zip is referred to in index, so that file (at least) should be retained for ease of distribution.

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Simple extraction of the files from files/snakemake-lesson.zip, with a new rule to build that file from modified sources as necessary. LGTM.

@psteinb psteinb merged commit 7cfa141 into hpc-carpentry:gh-pages Dec 17, 2019
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2 participants