recipe conipher

CONIPHER is an R package for clustering mutation data and reconstruction of tumor phylogenetic trees from DNA sequencing.

Homepage:

https://github.com/McGranahanLab/CONIPHER/

License:

BSD-3-Clause

Recipe:

/conipher/meta.yaml

Links:

doi: 10.1038/s41596-023-00913-9

package conipher

versions:

2.2.0-0,  2.1.0-1,  2.1.0-0

depends pyclone:

depends r-base:

>=4.0,<4.1.0a0

depends r-beeswarm:

depends r-biocmanager:

depends r-boot:

depends r-bootstrap:

depends r-catools:

depends r-coin:

depends r-cowplot:

depends r-devtools:

depends r-fst:

depends r-ggpubr:

depends r-gplots:

depends r-gtools:

depends r-igraph:

depends r-kernsmooth:

depends r-mapplots:

depends r-optparse:

depends r-parallelly:

depends r-rcolorbrewer:

depends r-tidyverse:

depends r-wordcloud:

requirements:

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 conipher

and update with::

   mamba update conipher

To create a new environment, run:

mamba create --name myenvname conipher

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/conipher:<tag>

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

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