recipe weeder

Motif (transcription factor binding sites) discovery in sequences from coregulated genes of a single species. This is a new Weeder release rewritten to be faster and optimized for large ChIP-Seq data.

Homepage:

http://159.149.160.51/modtools/

License:

GPL3

Recipe:

/weeder/meta.yaml

Links:

biotools: weeder, doi: 10.1002/0471250953.bi0211s47

package weeder

(downloads) docker_weeder

versions:
2.0-10,  2.0-9,  2.0-8,  2.0-7,  2.0-6,  2.0-5,  2.0-4,  2.0-3,  2.0-2, 

2.0-10,  2.0-9,  2.0-8,  2.0-7,  2.0-6,  2.0-5,  2.0-4,  2.0-3,  2.0-2,  2.0-1,  2.0-0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends python:

requirements:

additional platforms:
linux-aarch64

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 weeder

and update with::

   mamba update weeder

To create a new environment, run:

mamba create --name myenvname weeder

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/weeder:<tag>

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

Notes

Includes a simple wrapper script to be able to run weeder from any directory. It passes arguments transparently to the weeder2 executable.

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