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Add jvarkit (the new toolkit with central dispatcher) #42902

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merged 5 commits into from
Sep 10, 2023

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DrYak
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@DrYak DrYak commented Sep 7, 2023

This is a new recipe for jvarkit:

  • A big change in recent versions of jvarkit, is that it changed from separate per-tool commands and jars (as in the old jvarkit-* bioconda packages) to a single central dispatcher.

i.e.: you don't run bamstat04 anymore like in package jvarkit-bamstat04, now you run jvarkit bamstat04 as per latest docs

I've added a bunch of symlinked wrappers for the old-style single commands, so hopefully people who relied on the old jvarkit-* packages should be able to switch?


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- note that recent version of the jvartools have changed from
  separate per-tool command (as in the old jvarkit-* packages)
  to a single central dispatcher
- NOTE some lack of quotes (") is intentionally *for* splitting
@DrYak
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DrYak commented Sep 7, 2023

@BiocondaBot please fetch artifacts

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DrYak commented Sep 7, 2023

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Sep 7, 2023
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Package(s) built on Azure are ready for inspection:

Arch Package Zip File
noarch jvarkit-2023.09.07-hdfd78af_0.tar.bz2 LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package Tag Install with docker
jvarkit 2023.09.07--hdfd78af_0
showgzip -dc LinuxArtifacts/images/jvarkit:2023.09.07--hdfd78af_0.tar.gz | docker load

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mencian commented Sep 10, 2023

Thanks! @DrYak

@mencian mencian merged commit f67794b into bioconda:master Sep 10, 2023
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3 participants