- recipe stacks
Stacks is a software pipeline for building loci from RAD-seq
- Homepage:
- License:
GPL
- Recipe:
- Links:
biotools: Stacks, doi: 10.1111/mec.12354
- package stacks¶
- versions:
2.65-0
,2.64-0
,2.61-1
,2.61-0
,2.60-1
,2.60-0
,2.55-1
,2.55-0
,2.53-1
,2.65-0
,2.64-0
,2.61-1
,2.61-0
,2.60-1
,2.60-0
,2.55-1
,2.55-0
,2.53-1
,2.53-0
,2.52-0
,2.5-0
,2.4-1
,2.4-0
,2.3-6
,2.3-5
,2.3-4
,2.3-3
,2.3d-1
,2.3d-0
,2.3c-3
,2.3c-2
,2.3c-1
,2.3c-0
,2.3b-3
,2.3b-2
,2.3b-1
,2.3b-0
,2.2-6
,2.2-5
,2.2-4
,2.2-3
,2.2-2
,2.2-1
,2.2-0
,2.1-5
,2.1-4
,2.1-3
,2.1-2
,2.1-1
,2.0-4
,2.0-3
,2.0-2
,2.0-1
,2.0-0
,2.0Beta10a-0
,2.0Beta9-0
,2.0Beta8-1
,2.0Beta8-0
,2.0Beta8c-1
,2.0Beta8c-0
,2.0Beta7c-0
,1.48-1
,1.48-0
,1.47-2
,1.47-1
,1.47-0
,1.46-4
,1.46-3
,1.46-2
,1.46-1
,1.46-0
,1.44-3
,1.44-2
,1.44-1
,1.44-0
,1.43-2
,1.43-1
,1.43-0
,1.42-5
,1.42-4
,1.42-3
,1.42-2
,1.42-1
,1.40-3
,1.40-2
,1.40-1
,1.40-0
,1.37-5
,1.37-4
,1.37-3
,1.37-2
,1.37-1
,1.37-0
- depends libgcc-ng:
>=12
- depends libstdcxx-ng:
>=12
- depends libzlib:
>=1.2.13,<1.3.0a0
- depends openmp:
- depends perl:
- depends perl-bioperl-core:
- depends perl-file-spec:
- depends perl-file-temp:
- depends perl-posix:
- depends python:
>=3
- depends r-base:
>=4
- depends samtools:
- depends velvet:
- depends zlib:
- 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 stacks and update with:: mamba update stacks
To create a new environment, run:
mamba create --name myenvname stacks
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/stacks:<tag> (see `stacks/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/stacks/README.html)