recipe snp-pileup

Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets

Homepage:

https://github.com/mskcc/facets

License:

MIT / MIT

Recipe:

/snp-pileup/meta.yaml

package snp-pileup

versions:

0.6.2-8,  0.6.2-7,  0.6.2-6,  0.6.2-5,  0.6.2-4,  0.6.2-3,  0.6.2-2,  0.6.2-1,  0.6.2-0, 

0.6.2-8,  0.6.2-7,  0.6.2-6,  0.6.2-5,  0.6.2-4,  0.6.2-3,  0.6.2-2,  0.6.2-1,  0.6.2-0,  0.6.1-1,  0.6.1-0,  0.5.14-3,  0.5.14-2,  0.5.14-1,  0.5.14-0,  v0.5.14-0

depends htslib:

>=1.21,<1.22.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

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 snp-pileup

and update with::

   mamba update snp-pileup

To create a new environment, run:

mamba create --name myenvname snp-pileup

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/snp-pileup:<tag>

(see `snp-pileup/tags`_ for valid values for ``<tag>``)

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