recipe nanosim

NanoSim is a fast and scalable read simulator for Nanopore sequencing data.

Homepage:

https://github.com/bcgsc/NanoSim

License:

GPL3 / GPL-3.0-only

Recipe:

/nanosim/meta.yaml

Links:

doi: 10.1093/gigascience/gix010, doi: 10.1093/gigascience/giaa061

package nanosim

versions:

3.2.2-0,  3.2.1-1,  3.2.1-0,  3.2.0-2,  3.2.0-1,  3.2.0-0,  3.1.0-0,  3.0.2-0,  3.0.0-0, 

3.2.2-0,  3.2.1-1,  3.2.1-0,  3.2.0-2,  3.2.0-1,  3.2.0-0,  3.1.0-0,  3.0.2-0,  3.0.0-0,  2.6.0-1,  2.6.0-0,  2.5.1-1,  2.5.1-0,  2.5.0-0,  2.2.0-0,  2.1.0-0,  2.0.0-1,  2.0.0-0,  v1.3.0-0,  v1.2.0-0,  v1.0.1-1

depends genometools-genometools:

depends htseq:

>=0.9.1

depends joblib:

depends last:

depends minimap2:

>=2.18

depends numpy:

>=1.13.3

depends piecewise-regression:

depends pybedtools:

>=0.7.10

depends pysam:

>=0.13

depends python:

depends regex:

depends sam2pairwise:

depends samtools:

depends scikit-learn:

>=0.20.0

depends scipy:

>=1.0.0

depends six:

>=1.10.0

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 nanosim

and update with::

   mamba update nanosim

To create a new environment, run:

mamba create --name myenvname nanosim

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/nanosim:<tag>

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

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