recipe khmer

khmer k-mer counting library.

Homepage:

https://github.com/dib-lab/khmer

Documentation:

https://khmer.readthedocs.io

License:

BSD / BSD-3-License

Recipe:

/khmer/meta.yaml

Links:

biotools: khmer, doi: 10.12688/f1000research.6924.1, usegalaxy-eu: khmer_filter_abundance, usegalaxy-eu: khmer_filter_below_abundance_cutoff, usegalaxy-eu: khmer_extract_partitions, usegalaxy-eu: khmer_abundance_distribution, usegalaxy-eu: khmer_count_median, usegalaxy-eu: khmer_partition, usegalaxy-eu: khmer_normalize_by_median, usegalaxy-eu: khmer_abundance_distribution_single

package khmer

(downloads) docker_khmer

versions:
3.0.0a3-7,  3.0.0a3-6,  3.0.0a3-3,  3.0.0a3-2,  3.0.0a3-1,  3.0.0a3-0,  3.0.0a2-1,  3.0.0a2-0,  3.0.0a1-0, 

3.0.0a3-7,  3.0.0a3-6,  3.0.0a3-3,  3.0.0a3-2,  3.0.0a3-1,  3.0.0a3-0,  3.0.0a2-1,  3.0.0a2-0,  3.0.0a1-0,  2.1.2-0,  2.1-0,  2.1rc1-0,  2.0-2,  2.0-1,  2.0-0

depends _openmp_mutex:

>=4.5

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc:

depends libgcc-ng:

>=12

depends libgomp:

depends libstdcxx:

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.3.1,<2.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends screed:

>=1.0

requirements:

additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install khmer

and update with::

   mamba update khmer

To create a new environment, run:

mamba create --name myenvname khmer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/khmer:<tag>

(see `khmer/tags`_ for valid values for ``<tag>``)

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