- recipe nanovar
Structural variant caller using low-depth long reads
- Homepage:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
- package nanovar¶
- versions:
1.8.1-0,1.8.0-0,1.5.1-0,1.5.0-0,1.4.1-2,1.4.1-1,1.4.1-0,1.4.0-0,1.3.9-1,1.8.1-0,1.8.0-0,1.5.1-0,1.5.0-0,1.4.1-2,1.4.1-1,1.4.1-0,1.4.0-0,1.3.9-1,1.3.9-0,1.3.8-1,1.3.8-0,1.3.6-0,1.3.5-0,1.3.4-0,1.3.2-0,1.3.1-0,1.3.0-0,1.2.7-0,1.2.6-0,1.2.5-0,1.2.3-0- depends bedtools:
>=2.26.0- depends biopython:
>=1.82- depends bs4:
>=0.0.2- depends libgcc:
>=12- depends matplotlib-base:
>=2.2.3- depends minimap2:
>=2.17- depends natsort:
>=6.2.0- depends numpy:
>=1.17.3,<2.0.0- depends pybedtools:
>=0.8.2- depends pysam:
>=0.15.3- depends python:
>=3.8,<3.9.0a0- depends python_abi:
3.8.* *_cp38- depends samtools:
>=1.3- depends scipy:
>=1.2.1- depends tensorflow-cpu:
>=2.0.0,<=2.15.1- 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 nanovar and update with:: mamba update nanovar
To create a new environment, run:
mamba create --name myenvname nanovar
with
myenvnamebeing 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/nanovar:<tag> (see `nanovar/tags`_ for valid values for ``<tag>``)
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Link to this page¶
Render an 
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