recipe cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells.

Homepage:

https://github.com/single-cell-genetics/cellsnp-lite

Documentation:

https://cellsnp-lite.readthedocs.io/en/latest

License:

APACHE / Apache-2.0

Recipe:

/cellsnp-lite/meta.yaml

Links:

doi: 10.1093/bioinformatics/btab358, biotools: cellsnp-lite

package cellsnp-lite

(downloads) docker_cellsnp-lite

versions:
1.2.3-4,  1.2.3-3,  1.2.3-2,  1.2.3-1,  1.2.3-0,  1.2.2-3,  1.2.2-2,  1.2.2-1,  1.2.2-0, 

1.2.3-4,  1.2.3-3,  1.2.3-2,  1.2.3-1,  1.2.3-0,  1.2.2-3,  1.2.2-2,  1.2.2-1,  1.2.2-0,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.0.1-0,  1.0.0-1,  1.0.0-0,  0.3.1-1,  0.3.1-0

depends bzip2:

>=1.0.8,<2.0a0

depends htslib:

>=1.20,<1.23.0a0

depends libcurl:

>=8.8.0,<9.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<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 cellsnp-lite

and update with::

   mamba update cellsnp-lite

To create a new environment, run:

mamba create --name myenvname cellsnp-lite

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/cellsnp-lite:<tag>

(see `cellsnp-lite/tags`_ for valid values for ``<tag>``)

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Link to this page

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