recipe captus

Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data.

Homepage:

https://github.com/edgardomortiz/Captus

Documentation:

https://edgardomortiz.github.io/captus.docs

License:

GPL3 / GPL-3.0-only

Recipe:

/captus/meta.yaml

Links:

doi: 10.1101/2023.10.27.564367

package captus

versions:

1.4.1-0,  1.4.0-0,  1.3.9-0,  1.3.8-0,  1.3.7-0,  1.3.6-0,  1.3.4-0,  1.3.3-0,  1.3.2-0, 

1.4.1-0,  1.4.0-0,  1.3.9-0,  1.3.8-0,  1.3.7-0,  1.3.6-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.9.99-0,  0.9.98-0,  0.9.97-0,  0.9.96-0,  0.9.95-2,  0.9.95-1,  0.9.95-0,  0.9.93-0,  0.9.92-0,  0.9.91-2,  0.9.91-0,  0.9.90-0,  0.9.89-0,  0.9.88-1,  0.9.88-0,  0.9.86-0,  0.9.85-0,  0.9.84-1,  0.9.84-0,  0.9.83-0

depends bbmap:

depends clipkit:

>=1.3.0

depends falco:

>=0.3.0

depends fastqc:

depends mafft:

depends megahit:

>=1.2.9

depends mmseqs2:

depends muscle:

>=5

depends pandas:

>=2.1.0

depends perl-bioperl-core:

depends perl-yaml:

depends pigz:

depends plotly:

depends python:

>=3.6

depends salmon:

>=1.10.0

depends tqdm:

depends vsearch:

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 captus

and update with::

   mamba update captus

To create a new environment, run:

mamba create --name myenvname captus

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/captus:<tag>

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

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