recipe ntedit

Ultrafast, lightweight, scalable genome assembly polishing, and SNV detection & annotation

Homepage:

https://github.com/bcgsc/ntEdit

Documentation:

https://github.com/bcgsc/ntEdit/blob/master/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/ntedit/meta.yaml

Links:

doi: 10.1093/bioinformatics/btz400, biotools: ntEdit

package ntedit

(downloads) docker_ntedit

versions:
2.1.1-0,  2.1.0-1,  2.1.0-0,  2.0.3-0,  2.0.2-2,  2.0.2-1,  2.0.2-0,  2.0.1-1,  2.0.1-0, 

2.1.1-0,  2.1.0-1,  2.1.0-0,  2.0.3-0,  2.0.2-2,  2.0.2-1,  2.0.2-0,  2.0.1-1,  2.0.1-0,  2.0.0-0,  1.4.3-0,  1.3.5-4,  1.3.5-3,  1.3.5-2,  1.3.5-1,  1.3.5-0,  1.3.4-1,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0

depends boost-cpp:

depends btllib:

>=1.7.3,<2.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends ntcard:

depends ntstat:

>=1.0.1

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends python_abi:

3.12.* *_cp312

depends snakemake-minimal:

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 ntedit

and update with::

   mamba update ntedit

To create a new environment, run:

mamba create --name myenvname ntedit

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/ntedit:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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