Package Recipe 'eden'

recipe eden

The Explicit Decomposition with Neighborhoods (EDeN) is a decompositional kernel based on the Neighborhood Subgraph Pairwise Distance Kernel (NSPDK) that can be used to induce an explicit feature representation for graphs. This in turn allows the adoption of machine learning algorithm to perform supervised and unsupervised learning task in a scalable way (e.g. using fast stochastic gradient descent methods in classification and approximate neighborhood queries in clustering).

Homepage:: https://github.com/fabriziocosta/EDeN
License:: MIT
Recipe:: /eden/meta.yaml

package eden¶

Versions:

2.0-3, 2.0-2, 2.0-1, 2.0-0, 1.1-5, 1.1-4, 1.1-3, 1.1-2, 1.1-1,

2.0-3, 2.0-2, 2.0-1, 2.0-0, 1.1-5, 1.1-4, 1.1-3, 1.1-2, 1.1-1, 1.1-0

Depends:

on biopython
on cvxopt
on dill
on esmre
on joblib
on matplotlib
on muscle
on networkx <=1.10
on numpy
on openbabel
on pandas
on pybedtools
on python <3
on python-graphviz
on rdkit
on reportlab
on requests
on rnashapes
on scikit-learn >=0.17.0,<0.20.0
on scipy >=0.14.0
on weblogo

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 eden

to add into an existing workspace instead, run:

pixi add eden

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 eden

Alternatively, to install into a new environment, run:

conda create -n envname eden

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/eden:<tag>

(see eden/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/eden/README.html)