recipe kmer-jellyfish

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.

Homepage:

https://genome.umd.edu/jellyfish.html

Documentation:

https://genome.umd.edu/docs/JellyfishUserGuide.pdf

Developer docs:

https://github.com/gmarcais/Jellyfish

License:

GPL3 / GPL-3.0-or-later

Recipe:

/kmer-jellyfish/meta.yaml

Links:

biotools: jellyfish, doi: 10.1093/bioinformatics/btr011, usegalaxy-eu: jellyfish

package kmer-jellyfish

versions:

2.3.1-5,  2.3.1-4,  2.3.1-3,  2.3.1-2,  2.3.1-1,  2.3.1-0,  2.3.0-3,  2.3.0-2,  2.3.0-1, 

2.3.1-5,  2.3.1-4,  2.3.1-3,  2.3.1-2,  2.3.1-1,  2.3.1-0,  2.3.0-3,  2.3.0-2,  2.3.0-1,  2.3.0-0,  1.1.12-4,  1.1.12-2,  1.1.12-1,  1.1.12-0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends yaggo:

>=1.5.10,<1.6.0a0

requirements:

additional platforms:

linux-aarch64

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 kmer-jellyfish

and update with::

   mamba update kmer-jellyfish

To create a new environment, run:

mamba create --name myenvname kmer-jellyfish

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/kmer-jellyfish:<tag>

(see `kmer-jellyfish/tags`_ for valid values for ``<tag>``)

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