recipe lepwrap

The Snakemake pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring+orienting genome assemblies.

Homepage:

https://github.com/pdimens/LepWrap/

License:

The GNU General Public License v3.0 (GPL3)

Recipe:

/lepwrap/meta.yaml

package lepwrap

versions:

4.0.1-0,  4.0-0

depends bzip2:

depends font-ttf-dejavu-sans-mono:

depends font-ttf-ubuntu:

depends graphviz:

depends imagemagick:

depends openjdk:

depends pandoc:

depends pygraphviz:

depends python:

>=3.9

depends r-base:

>=4

depends r-dplyr:

depends r-ggplot2:

depends r-readr:

depends r-stringr:

depends r-tidyr:

depends sed:

depends snakemake:

>=6.4

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 lepwrap

and update with::

   mamba update lepwrap

To create a new environment, run:

mamba create --name myenvname lepwrap

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/lepwrap:<tag>

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

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