recipe segalign-galaxy

SegAlign: A Scalable GPU-Based Whole Genome Aligner

Homepage:

https://github.com/galaxyproject/SegAlign

Documentation:

https://github.com/galaxyproject/SegAlign/blob/main/README.md

License:

MIT / MIT

Recipe:

/segalign-galaxy/meta.yaml

Links:

doi: 10.1109/SC41405.2020.00043, doi: 10.5281/zenodo.3880947

SegAlign is a Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.

package segalign-galaxy

(downloads) docker_segalign-galaxy

versions:

0.1.2.7-2,  0.1.2.7-1,  0.1.2.7-0

depends bashlex:

depends gzip:

depends python:

3.12.*

depends segalign-full:

0.1.2.7.*

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 segalign-galaxy

and update with::

   mamba update segalign-galaxy

To create a new environment, run:

mamba create --name myenvname segalign-galaxy

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/segalign-galaxy:<tag>

(see `segalign-galaxy/tags`_ for valid values for ``<tag>``)

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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/segalign-galaxy/README.html)