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Add a recipe for glean-gene #53156

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Jan 9, 2025
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@martin-g martin-g commented Jan 9, 2025

GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

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GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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martin-g commented Jan 9, 2025

@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch glean-gene-1.0.1-hdfd78af_0.tar.bz2 noarch.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
glean-gene 1.0.1--hdfd78af_0 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/glean-gene---1.0.1--hdfd78af_0.tar.gz | docker load

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martin-g commented Jan 9, 2025

@aliciaaevans How much work would it be to have two artifacts for the Github builds - the current Docker file and just the Conda package ?
My problem at the moment is that this simple noarch recipe produces a file with size of 1.2GB.
I'd like to test only the Conda package (few KB, that could be downloaded in few seconds).

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martin-g commented Jan 9, 2025

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jan 9, 2025
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@martin-g In addition to changing the workflow yaml to upload separate artifact files, we'd have to make some changes to bioconda-utils to handle it for the upload to the channel when master is merged. Nothing too time-consuming, just a matter of someone getting around to it.

Changes would be in this file if you or anyone else want to take it on:
https://github.com/bioconda/bioconda-utils/blob/fcaf2913238ecf19e898da29676c7db107d1d539/bioconda_utils/artifacts.py#L31
And then the BiocondaBot artifacts comment would need to change: https://github.com/bioconda/bioconda-containers/blob/7b022b17af3f18619b629c1ee13df151c66b7fb8/images/bot/src/bioconda_bot/comment.py#L126

@aliciaaevans aliciaaevans merged commit 0cedc43 into bioconda:master Jan 9, 2025
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@martin-g martin-g deleted the glean-gene branch January 9, 2025 15:49
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