Package Recipe 'nanopore_simulation'

recipe nanopore_simulation

Nanopore SimulatION is a tool for simulating an Oxfornd Nanopore Technologies MinION device for bioinformatic development.

Homepage:: https://github.com/crohrandt/nanopore_simulation
License:: MPL-2.0
Recipe:: /nanopore_simulation/meta.yaml

package nanopore_simulation¶

Versions:

0.3-2, 0.3-1, 0.3-0

Depends:

on biopython
on h5py
on matplotlib
on numpy
on pandas
on python >=3
on scipy

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install nanopore_simulation

to add into an existing workspace instead, run:

pixi add nanopore_simulation

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install nanopore_simulation

Alternatively, to install into a new environment, run:

conda create -n envname nanopore_simulation

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/nanopore_simulation:<tag>

(see nanopore_simulation/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/nanopore_simulation/README.html)