Package Recipe 'fastspar'

recipe fastspar

Rapid and scalable correlation estimation for compositional data

Homepage:: https://github.com/scwatts/fastspar
License:: GPLv3
Recipe:: /fastspar/meta.yaml
Links:: doi: 10.1093/bioinformatics/bty734, doi: 10.1371/journal.pcbi.1002687

FastSpar is a C++ implementation of the SparCC algorithm which is up to several thousand times faster than the original Python2 release and uses much less memory. The FastSpar implementation provides threading support and a p-value estimator which accounts for the possibility of repetitious data permutations.

package fastspar¶

Versions:

1.0.0-6, 1.0.0-5, 1.0.0-4, 1.0.0-3, 1.0.0-2, 1.0.0-1, 1.0.0-0, 0.0.10-0, 0.0.9-0,

1.0.0-6, 1.0.0-5, 1.0.0-4, 1.0.0-3, 1.0.0-2, 1.0.0-1, 1.0.0-0, 0.0.10-0, 0.0.9-0, 0.0.6-0

Depends:

on armadillo >=14.2,<15.0a0
on armadillo >=7.800.1
on gsl >=2.7,<2.8.0a0
on libgcc >=13
on libgfortran
on libgfortran5 >=13.3.0
on libstdcxx >=13
on openblas * *openmp*

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 fastspar

to add into an existing workspace instead, run:

pixi add fastspar

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 fastspar

Alternatively, to install into a new environment, run:

conda create -n envname fastspar

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/fastspar:<tag>

(see fastspar/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/fastspar/README.html)