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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.
The text was updated successfully, but these errors were encountered:
Only kraken2, kraken2-build, and kraken2-inspect are copied to the conda environment bin directory during the build and therefore in the $PATH for users, k2 should also be copied, but I would say you should probably rename it to kraken2-k2 or something so it will be easily distinguishable in the environment with other packages, and so it doesn't accidentally clobber something else that could have the same short name.
What I recently discovered is that some published Kraken2 functionality (#855) is only available if you run commands via the
k2
script, not the traditional binaries likekraken2-build
.But the
k2
script isn't in the$PATH
in the Biocondakraken2
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 thekraken2
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.The text was updated successfully, but these errors were encountered: