recipe stacks

Stacks is a software pipeline for building loci from RAD-seq

Homepage:

https://catchenlab.life.illinois.edu/stacks/

License:

GPL

Recipe:

/stacks/meta.yaml

Links:

biotools: Stacks, doi: 10.1111/mec.12354

package stacks

versions:

2.65-1,  2.65-0,  2.64-0,  2.61-1,  2.61-0,  2.60-1,  2.60-0,  2.55-1,  2.55-0, 

2.65-1,  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,  1.48-2,  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:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

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>``)

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