recipe cawlign

A tool for aligning consensus sequences to reference genomes

Homepage:

https://github.com/veg/cawlign

License:

MIT / MIT

Recipe:

/cawlign/meta.yaml

A standalone C++ port of bealign, a part of the BioExt package. The purpose of this program is to align/map sequences in a FASTA file to a reference sequence and output the alignment as another FASTA file.

Key features: * Lightweight and self-contained * Allows codon-aware alignment while handling out-of-frame events * Flexible specification of scoring matrices * OpenMP support

package cawlign

versions:

0.1.11-0

depends _openmp_mutex:

>=4.5

depends libcurl:

>=8.13.0,<9.0a0

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends openmpi:

>=4.1.6,<5.0a0

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 cawlign

and update with::

   mamba update cawlign

To create a new environment, run:

mamba create --name myenvname cawlign

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/cawlign:<tag>

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

Download stats

Link to this page

Render an 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/cawlign/README.html)