recipe nanomonsv

Python tools for detecting structural variation from nanopore sequence data

Homepage:

https://github.com/friend1ws/nanomonsv

License:

GPL-3.0

Recipe:

/nanomonsv/meta.yaml

package nanomonsv

versions:

0.7.2-0,  0.7.0-0,  0.6.0-0,  0.5.1-0,  0.5.0-0

depends bedtools:

>=2.30.0

depends bwa:

>=0.7.17

depends htslib:

depends mafft:

>=7.407

depends minimap2:

>=2.24

depends numpy:

>=1.23.0

depends parasail-python:

>=1.2.4

depends pysam:

>=0.19.1

depends python:

>=3.6

depends racon:

>=1.4.3

depends repeatmasker:

>=4.1.1

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 nanomonsv

and update with::

   mamba update nanomonsv

To create a new environment, run:

mamba create --name myenvname nanomonsv

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/nanomonsv:<tag>

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

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