recipe lassaseq

Tool for downloading Lassa virus sequences

Homepage:

https://github.com/DaanJansen94/LassaSeq

Documentation:

https://github.com/DaanJansen94/LassaSeq/blob/master/README.md

License:

GPL / GPL-3.0

Recipe:

/lassaseq/meta.yaml

LassaSeq is a command-line tool that simplifies the process of analyzing Lassa virus sequences. It automates the complete workflow from downloading sequences to creating phylogenetic trees, with special handling for Lassa's bi-segmented genome.

package lassaseq

(downloads) docker_lassaseq

versions:

0.1.2-0,  0.1.1-0,  0.1.0-0

depends biopython:

>=1.80

depends iqtree:

depends mafft:

depends numpy:

>=1.20.0

depends python:

>=3.9

depends requests:

>=2.25.0

depends tqdm:

>=4.50.0

depends trimal:

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 lassaseq

and update with::

   mamba update lassaseq

To create a new environment, run:

mamba create --name myenvname lassaseq

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/lassaseq:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/lassaseq/README.html)