Commit | Line | Data |
---|---|---|
e57fffad | 1 | ;;; GNU Guix --- Functional package management for GNU |
4e35c429 | 2 | ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net> |
e57fffad RW |
3 | ;;; |
4 | ;;; This file is part of GNU Guix. | |
5 | ;;; | |
6 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
7 | ;;; under the terms of the GNU General Public License as published by | |
8 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
9 | ;;; your option) any later version. | |
10 | ;;; | |
11 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
12 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
14 | ;;; GNU General Public License for more details. | |
15 | ;;; | |
16 | ;;; You should have received a copy of the GNU General Public License | |
17 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
18 | ||
19 | (define-module (gnu packages graph) | |
20 | #:use-module (guix download) | |
4e35c429 | 21 | #:use-module (guix git-download) |
e57fffad RW |
22 | #:use-module (guix packages) |
23 | #:use-module (guix build-system gnu) | |
31476df3 | 24 | #:use-module (guix build-system python) |
1738138c | 25 | #:use-module (guix build-system r) |
e57fffad RW |
26 | #:use-module ((guix licenses) #:prefix license:) |
27 | #:use-module (gnu packages) | |
1738138c | 28 | #:use-module (gnu packages gcc) |
e206de67 | 29 | #:use-module (gnu packages bioinformatics) |
e57fffad | 30 | #:use-module (gnu packages compression) |
fff9b884 | 31 | #:use-module (gnu packages cran) |
e206de67 | 32 | #:use-module (gnu packages graphviz) |
e57fffad RW |
33 | #:use-module (gnu packages maths) |
34 | #:use-module (gnu packages multiprecision) | |
31476df3 | 35 | #:use-module (gnu packages pkg-config) |
1738138c | 36 | #:use-module (gnu packages statistics) |
e57fffad RW |
37 | #:use-module (gnu packages xml)) |
38 | ||
39 | (define-public igraph | |
40 | (package | |
41 | (name "igraph") | |
42 | (version "0.7.1") | |
43 | (source | |
44 | (origin | |
45 | (method url-fetch) | |
46 | (uri (string-append "http://igraph.org/nightly/get/c/igraph-" | |
47 | version ".tar.gz")) | |
48 | (sha256 | |
49 | (base32 | |
50 | "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r")))) | |
51 | (build-system gnu-build-system) | |
52 | (arguments | |
53 | `(#:configure-flags | |
54 | (list "--with-external-glpk" | |
55 | "--with-external-blas" | |
56 | "--with-external-lapack"))) | |
57 | (inputs | |
58 | `(("gmp" ,gmp) | |
59 | ("glpk" ,glpk) | |
60 | ("libxml2" ,libxml2) | |
61 | ("lapack" ,lapack) | |
62 | ("openblas" ,openblas) | |
63 | ("zlib" ,zlib))) | |
64 | (home-page "http://igraph.org") | |
65 | (synopsis "Network analysis and visualization") | |
66 | (description | |
67 | "This package provides a library for the analysis of networks and graphs. | |
68 | It can handle large graphs very well and provides functions for generating | |
69 | random and regular graphs, graph visualization, centrality methods and much | |
70 | more.") | |
71 | (license license:gpl2+))) | |
31476df3 RW |
72 | |
73 | (define-public python-igraph | |
74 | (package (inherit igraph) | |
75 | (name "python-igraph") | |
76 | (version "0.7.1.post6") | |
77 | (source | |
78 | (origin | |
79 | (method url-fetch) | |
80 | (uri (pypi-uri "python-igraph" version)) | |
81 | (sha256 | |
82 | (base32 | |
83 | "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5")))) | |
84 | (build-system python-build-system) | |
85 | (arguments '()) | |
86 | (inputs | |
87 | `(("igraph" ,igraph))) | |
88 | (native-inputs | |
89 | `(("pkg-config" ,pkg-config))) | |
90 | (home-page "http://pypi.python.org/pypi/python-igraph") | |
91 | (synopsis "Python bindings for the igraph network analysis library"))) | |
1738138c RW |
92 | |
93 | (define-public r-igraph | |
94 | (package | |
95 | (name "r-igraph") | |
96 | (version "1.1.2") | |
97 | (source | |
98 | (origin | |
99 | (method url-fetch) | |
100 | (uri (cran-uri "igraph" version)) | |
101 | (sha256 | |
102 | (base32 | |
103 | "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) | |
104 | (build-system r-build-system) | |
105 | (native-inputs | |
106 | `(("gfortran" ,gfortran))) | |
107 | (inputs | |
108 | `(("gmp" ,gmp) | |
109 | ("libxml2" ,libxml2))) | |
110 | (propagated-inputs | |
111 | `(("r-irlba" ,r-irlba) | |
112 | ("r-magrittr" ,r-magrittr) | |
113 | ("r-matrix" ,r-matrix) | |
114 | ("r-pkgconfig" ,r-pkgconfig))) | |
115 | (home-page "http://igraph.org") | |
116 | (synopsis "Network analysis and visualization") | |
117 | (description | |
118 | "This package provides routines for simple graphs and network analysis. | |
119 | It can handle large graphs very well and provides functions for generating | |
120 | random and regular graphs, graph visualization, centrality methods and much | |
121 | more.") | |
122 | (license license:gpl2+))) | |
e206de67 | 123 | |
fff9b884 RW |
124 | (define-public r-diffusionmap |
125 | (package | |
126 | (name "r-diffusionmap") | |
127 | (version "1.1-0") | |
128 | (source | |
129 | (origin | |
130 | (method url-fetch) | |
131 | (uri (cran-uri "diffusionMap" version)) | |
132 | (sha256 | |
133 | (base32 | |
134 | "1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3")))) | |
135 | (properties `((upstream-name . "diffusionMap"))) | |
136 | (build-system r-build-system) | |
137 | (propagated-inputs | |
138 | `(("r-igraph" ,r-igraph) | |
139 | ("r-matrix" ,r-matrix) | |
140 | ("r-scatterplot3d" ,r-scatterplot3d))) | |
141 | (home-page "http://www.r-project.org") | |
142 | (synopsis "Diffusion map") | |
143 | (description "This package implements the diffusion map method of data | |
144 | parametrization, including creation and visualization of diffusion maps, | |
145 | clustering with diffusion K-means and regression using the adaptive regression | |
146 | model.") | |
147 | (license license:gpl2))) | |
148 | ||
e206de67 RW |
149 | (define-public r-rgraphviz |
150 | (package | |
151 | (name "r-rgraphviz") | |
8ca2b2b0 | 152 | (version "2.22.0") |
e206de67 RW |
153 | (source |
154 | (origin | |
155 | (method url-fetch) | |
156 | (uri (bioconductor-uri "Rgraphviz" version)) | |
157 | (sha256 | |
158 | (base32 | |
8ca2b2b0 | 159 | "1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv")))) |
e206de67 RW |
160 | (properties `((upstream-name . "Rgraphviz"))) |
161 | (build-system r-build-system) | |
162 | ;; FIXME: Rgraphviz bundles the sources of an older variant of | |
163 | ;; graphviz. It does not build with the latest version of graphviz, so | |
164 | ;; we do not add graphviz to the inputs. | |
165 | (inputs `(("zlib" ,zlib))) | |
166 | (propagated-inputs | |
167 | `(("r-graph" ,r-graph))) | |
168 | (native-inputs | |
169 | `(("pkg-config" ,pkg-config))) | |
170 | (home-page "http://bioconductor.org/packages/Rgraphviz") | |
171 | (synopsis "Plotting capabilities for R graph objects") | |
172 | (description | |
173 | "This package interfaces R with the graphviz library for plotting R graph | |
174 | objects from the @code{graph} package.") | |
175 | (license license:epl1.0))) | |
4e35c429 RW |
176 | |
177 | (define-public r-rbiofabric | |
178 | (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") | |
179 | (revision "1")) | |
180 | (package | |
181 | (name "r-rbiofabric") | |
182 | (version (string-append "0.3-" revision "." (string-take commit 7))) | |
183 | (source (origin | |
184 | (method git-fetch) | |
185 | (uri (git-reference | |
186 | (url "https://github.com/wjrl/RBioFabric.git") | |
187 | (commit commit))) | |
188 | (file-name (string-append name "-" version "-checkout")) | |
189 | (sha256 | |
190 | (base32 | |
191 | "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) | |
192 | (build-system r-build-system) | |
193 | (propagated-inputs | |
194 | `(("r-igraph" ,r-igraph))) | |
195 | (home-page "http://www.biofabric.org/") | |
196 | (synopsis "BioFabric network visualization") | |
197 | (description "This package provides an implementation of the function | |
198 | @code{bioFabric} for creating scalable network digrams where nodes are | |
199 | represented by horizontal lines, and edges are represented by vertical | |
200 | lines.") | |
201 | (license license:expat)))) |