recipe commec

commec: a free, open-source, globally available tool for DNA sequence screening

Homepage:

https://github.com/ibbis-screening/common-mechanism

Documentation:

https://github.com/ibbis-screening/common-mechanism/wiki

License:

MIT / MIT

Recipe:

/commec/meta.yaml

package commec

versions:

0.2.0-0,  0.1.2-0

depends bedtools:

depends biopython:

depends blast:

>=2.16

depends diamond:

>=2.1

depends emboss:

depends hmmer:

depends infernal:

depends numpy:

depends pandas:

depends parallel:

depends perl-list-moreutils:

depends pytaxonkit:

depends python:

depends taxonkit:

depends wget:

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 commec

and update with::

   mamba update commec

To create a new environment, run:

mamba create --name myenvname commec

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/commec:<tag>

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

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Link to this page

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