recipe coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.

Homepage:

https://github.com/fwhelan/coinfinder

License:

GPL / GPL-3.0-only

Recipe:

/coinfinder/meta.yaml

Links:

doi: 10.1101/859371

package coinfinder

versions:

1.2.1-3,  1.2.1-2,  1.2.1-1,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.7-0, 

1.2.1-3,  1.2.1-2,  1.2.1-1,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.1.0-1,  1.1.0-0,  1.0.7-0,  1.0.6-0,  1.0.5-1,  1.0.5-0,  1.0.4-2,  1.0.4-1,  1.0.4-0,  1.0.3-0,  1.0.2-1,  1.0.2-0,  1.0.1-0,  1.0.0-3,  1.0.0-2,  1.0.0-1,  1.0.0-0

depends _openmp_mutex:

>=4.5

depends bioconductor-ggtree:

>=2.0.0,<2.1.0

depends boost-cpp:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends r-ape:

>=5.4.1

depends r-base:

3.6.*

depends r-caper:

>=1.0.1

depends r-cowplot:

>=1.1.1

depends r-data.table:

>=1.14

depends r-dplyr:

>=1.0.2

depends r-flock:

>=0.7

depends r-future:

>=1.21

depends r-getopt:

>=1.20.3

depends r-ggplot2:

>=3.0.0

depends r-ggraph:

>=2.0.5

depends r-igraph:

>=1.2.6

depends r-magrittr:

>=2.0.1

depends r-phytools:

>=0.6_99

depends r-purrr:

>=0.3.4

depends r-rlang:

>=0.4.1

depends r-rvcheck:

>=0.1.8

depends r-tidyr:

>=1.1.2

depends r-tidytree:

>=0.2.6

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 coinfinder

and update with::

   mamba update coinfinder

To create a new environment, run:

mamba create --name myenvname coinfinder

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/coinfinder:<tag>

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

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