recipe msoma

mSOMA: Somatic Mutation Detection using a betabinomial null model

Homepage:

https://github.com/AkeyLab/mSOMA

Documentation:

https://akeylab.github.io/mSOMA/

License:

MIT / MIT

Recipe:

/msoma/meta.yaml

package msoma

versions:

0.1.0-0

depends bamutil:

depends bioconductor-biostrings:

depends bioconductor-qvalue:

depends bioconductor-survcomp:

depends click:

>=8.0

depends importlib_resources:

>=5.4

depends numpy:

>=1.19

depends pandas:

>=1.1

depends pysam:

>=0.19

depends python:

>=3.7.1

depends r-argparse:

depends r-base:

depends r-bbmle:

depends r-data.table:

depends r-dplyr:

depends r-r.utils:

depends r-tidyverse:

depends r-vgam:

depends samtools:

depends scipy:

>=1.5

depends statsmodels:

>=0.12

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 msoma

and update with::

   mamba update msoma

To create a new environment, run:

mamba create --name myenvname msoma

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/msoma:<tag>

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

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