recipe kma

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

Homepage:

https://bitbucket.org/genomicepidemiology/kma

Documentation:

https://bitbucket.org/genomicepidemiology/kma/src/1.5.0/README.md

License:

APACHE / Apache-2.0

Recipe:

/kma/meta.yaml

Links:

doi: 10.1186/s12859-018-2336-6, usegalaxy-eu: kma_map, biotools: kma

package kma

(downloads) docker_kma

versions:
1.5.0-0,  1.4.18-0,  1.4.17-0,  1.4.15-1,  1.4.15-0,  1.4.14-1,  1.4.14-0,  1.4.9-2,  1.4.9-1, 

1.5.0-0,  1.4.18-0,  1.4.17-0,  1.4.15-1,  1.4.15-0,  1.4.14-1,  1.4.14-0,  1.4.9-2,  1.4.9-1,  1.4.9-0,  1.4.3-1,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.28-1,  1.3.28-0,  1.3.27-0,  1.3.26-0,  1.3.25-0,  1.3.24-0,  1.3.23-0,  1.3.22-0,  1.3.21-0,  1.3.19-0,  1.3.18-0,  1.3.17-0,  1.3.15-0,  1.3.14-0,  1.3.13-1,  1.3.13-0,  1.3.12-0,  1.3.10-0,  1.3.9-0,  1.3.8-0,  1.3.7-0,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.0-0,  1.2.26-0,  1.2.25-0,  1.2.22-0,  1.2.21-0,  1.2.20-0,  1.2.19-0,  1.2.18-0,  1.2.17-0,  1.2.16-0,  1.2.15-0,  1.2.14-0,  1.2.12-0,  1.2.11-0,  1.2.9-0,  1.2.7-0,  1.2.6-0,  1.2.5-0,  1.2.3-0,  1.2.1-0,  1.2.0-0,  1.1.7-0,  1.0.1-0

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

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 kma

and update with::

   mamba update kma

To create a new environment, run:

mamba create --name myenvname kma

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/kma:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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