recipe souporcell

Clustering scRNAseq by genotypes.

Homepage:

https://github.com/wheaton5/souporcell

License:

MIT / MIT

Recipe:

/souporcell/meta.yaml

Links:

doi: 10.1101/699637v1, biotools: souporcell

package souporcell

versions:

2.5-0

depends bcftools:

>=1.9

depends bedtools:

>=2.28

depends freebayes:

>=1.3

depends hisat2:

depends htslib:

>=1.9

depends libgcc:

>=13

depends minimap2:

>=2.26

depends numpy:

depends pyfaidx:

depends pysam:

depends pystan:

<3

depends python:

depends pyvcf:

depends samtools:

>=1.9

depends scipy:

depends vartrix:

requirements:

additional platforms:

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 souporcell

and update with::

   mamba update souporcell

To create a new environment, run:

mamba create --name myenvname souporcell

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/souporcell:<tag>

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

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