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Bioconductor skeleton updates #169

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merged 8 commits into from Aug 25, 2017

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commented Aug 24, 2017

This PR moves the bioconductor_skeleton.py script from bioconda-recipes to bioconda-utils. It is now called with bioconda-utils bioconductor-skeleton.

Importantly, it also now handles data-heavy packages by building a post-link.sh script instead of a build.sh script. This is the strategy tested out in bioconda/bioconda-recipes#5485. The post-link script is executed at install-time, not build-time, which means the package data is not included in the conda package. This avoids consuming the limited space on the bioconda channel while still allowing large, data-heavy Bioconductor packages to be installed via conda.

Data packages are detected as those stored under the "data/annotation" subdirectory on the Bioconductor servers (e.g., http://bioconductor.org/packages/3.5/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz). This is automatically detected, so when building recipes you won't have to know or care ahead of time whether a package should use the post-link strategy.

xref bioconda/bioconda-recipes#5428

@daler daler referenced this pull request Aug 24, 2017

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Bioconductor data packages 1 #5854

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@daler daler merged commit ec14bf4 into master Aug 25, 2017

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@daler daler deleted the bioconductor-skeleton branch Aug 25, 2017

@johanneskoester

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commented Aug 25, 2017

This is simply amazing @daler! Yet another interesting story for our paper ;-).

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commented Aug 25, 2017

Thanks! I really needed those packages, glad we have a solution now. Hopefully this strategy will hold up to some real-world testing.

@bgruening

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commented Aug 25, 2017

I'm looking forward to some real work testing. I'm a little bit surprised that this small idea went through to smoothly I would have expected that the containers scream at us with running out of disc space :)

Thanks for implementing this! You rock!

@jerowe

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commented Aug 25, 2017

You are an infrastucture god, @daler. ;-)

@daler daler referenced this pull request Aug 25, 2017

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Bioconductor skeleton fixes #170

@Tomnl Tomnl referenced this pull request May 9, 2018

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add mspuritydata #8851

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