recipe gap2seq

Gap2Seq is a tool for filling gaps between contigs in genome assemblies.

Homepage:

https://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq/

License:

GPLv3

Recipe:

/gap2seq/meta.yaml

package gap2seq

versions:

3.1.1a-4,  3.1.1a-3,  3.1.1a-2,  3.1.1a-1,  3.1.1a-0,  3.1-3,  3.1-2,  3.1-1,  3.1-0, 

3.1.1a-4,  3.1.1a-3,  3.1.1a-2,  3.1.1a-1,  3.1.1a-0,  3.1-3,  3.1-2,  3.1-1,  3.1-0,  2.1-4,  2.1-3,  2.1-2,  2.1-1,  2.1-0,  2.0-8,  2.0-7,  2.0-6,  2.0-5,  2.0-4,  2.0-1

depends htslib:

>=1.20,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends zlib:

requirements:

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 gap2seq

and update with::

   mamba update gap2seq

To create a new environment, run:

mamba create --name myenvname gap2seq

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/gap2seq:<tag>

(see `gap2seq/tags`_ for valid values for ``<tag>``)

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