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Make k2 wrapper script available in $PATH in the Bioconda kraken2 package #857

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hermidalc opened this issue Jul 30, 2024 · 1 comment

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@hermidalc
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hermidalc commented Jul 30, 2024

What I recently discovered is that some published Kraken2 functionality (#855) is only available if you run commands via the k2 script, not the traditional binaries like kraken2-build.

But the k2 script isn't in the $PATH in the Bioconda kraken2 package and can only be found in a path deep in the user's conda environment, which isn't readily accessible in a portable way. Especially if you use the kraken2 package with Snakemake then the environment is in a path with a randomly generated directory name. Some users need to use Kraken2 in workflows using conda for reproducibility and distribution.

@hermidalc
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hermidalc commented Jul 30, 2024

Only kraken2, kraken2-build, and kraken2-inspect are copied to the conda environment bin directory during the build and therefore in the $PATH for users, k2 should also be copied, but I would say you should probably rename it to kraken2-k2 or something so it will be easily distinguishable in the environment with other packages, and so it doesn't accidentally clobber something else that could have the same short name.

k2 should be added to the for loop here:

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/kraken2/build.sh#L18

for bin in kraken2 kraken2-build kraken2-inspect; do

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