201 lines
6.9 KiB
Scheme
201 lines
6.9 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
|
|
;;;
|
|
;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages graph)
|
|
#:use-module (guix download)
|
|
#:use-module (guix git-download)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system python)
|
|
#:use-module (guix build-system r)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages bioinformatics)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages cran)
|
|
#:use-module (gnu packages graphviz)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages statistics)
|
|
#:use-module (gnu packages xml))
|
|
|
|
(define-public igraph
|
|
(package
|
|
(name "igraph")
|
|
(version "0.7.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://igraph.org/nightly/get/c/igraph-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "--with-external-glpk"
|
|
"--with-external-blas"
|
|
"--with-external-lapack")))
|
|
(inputs
|
|
`(("gmp" ,gmp)
|
|
("glpk" ,glpk)
|
|
("libxml2" ,libxml2)
|
|
("lapack" ,lapack)
|
|
("openblas" ,openblas)
|
|
("zlib" ,zlib)))
|
|
(home-page "http://igraph.org")
|
|
(synopsis "Network analysis and visualization")
|
|
(description
|
|
"This package provides a library for the analysis of networks and graphs.
|
|
It can handle large graphs very well and provides functions for generating
|
|
random and regular graphs, graph visualization, centrality methods and much
|
|
more.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public python-igraph
|
|
(package (inherit igraph)
|
|
(name "python-igraph")
|
|
(version "0.7.1.post6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "python-igraph" version))
|
|
(sha256
|
|
(base32
|
|
"0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
|
|
(build-system python-build-system)
|
|
(arguments '())
|
|
(inputs
|
|
`(("igraph" ,igraph)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://pypi.python.org/pypi/python-igraph")
|
|
(synopsis "Python bindings for the igraph network analysis library")))
|
|
|
|
(define-public r-igraph
|
|
(package
|
|
(name "r-igraph")
|
|
(version "1.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "igraph" version))
|
|
(sha256
|
|
(base32
|
|
"1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(inputs
|
|
`(("gmp" ,gmp)
|
|
("libxml2" ,libxml2)))
|
|
(propagated-inputs
|
|
`(("r-irlba" ,r-irlba)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-matrix" ,r-matrix)
|
|
("r-pkgconfig" ,r-pkgconfig)))
|
|
(home-page "http://igraph.org")
|
|
(synopsis "Network analysis and visualization")
|
|
(description
|
|
"This package provides routines for simple graphs and network analysis.
|
|
It can handle large graphs very well and provides functions for generating
|
|
random and regular graphs, graph visualization, centrality methods and much
|
|
more.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-diffusionmap
|
|
(package
|
|
(name "r-diffusionmap")
|
|
(version "1.1-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "diffusionMap" version))
|
|
(sha256
|
|
(base32
|
|
"1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3"))))
|
|
(properties `((upstream-name . "diffusionMap")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,r-igraph)
|
|
("r-matrix" ,r-matrix)
|
|
("r-scatterplot3d" ,r-scatterplot3d)))
|
|
(home-page "http://www.r-project.org")
|
|
(synopsis "Diffusion map")
|
|
(description "This package implements the diffusion map method of data
|
|
parametrization, including creation and visualization of diffusion maps,
|
|
clustering with diffusion K-means and regression using the adaptive regression
|
|
model.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rgraphviz
|
|
(package
|
|
(name "r-rgraphviz")
|
|
(version "2.22.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (bioconductor-uri "Rgraphviz" version))
|
|
(sha256
|
|
(base32
|
|
"1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
|
|
(properties `((upstream-name . "Rgraphviz")))
|
|
(build-system r-build-system)
|
|
;; FIXME: Rgraphviz bundles the sources of an older variant of
|
|
;; graphviz. It does not build with the latest version of graphviz, so
|
|
;; we do not add graphviz to the inputs.
|
|
(inputs `(("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-graph" ,r-graph)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://bioconductor.org/packages/Rgraphviz")
|
|
(synopsis "Plotting capabilities for R graph objects")
|
|
(description
|
|
"This package interfaces R with the graphviz library for plotting R graph
|
|
objects from the @code{graph} package.")
|
|
(license license:epl1.0)))
|
|
|
|
(define-public r-rbiofabric
|
|
(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
|
|
(revision "1"))
|
|
(package
|
|
(name "r-rbiofabric")
|
|
(version (string-append "0.3-" revision "." (string-take commit 7)))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/wjrl/RBioFabric.git")
|
|
(commit commit)))
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
(sha256
|
|
(base32
|
|
"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,r-igraph)))
|
|
(home-page "http://www.biofabric.org/")
|
|
(synopsis "BioFabric network visualization")
|
|
(description "This package provides an implementation of the function
|
|
@code{bioFabric} for creating scalable network digrams where nodes are
|
|
represented by horizontal lines, and edges are represented by vertical
|
|
lines.")
|
|
(license license:expat))))
|