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authorPjotr Prins2016-03-01 06:46:15 +0100
committerPjotr Prins2016-03-01 06:46:15 +0100
commitc8f84f11abaf1a7945dd704e518a7947136f629b (patch)
tree813d0f7c71a20998da51ef17bbba908be4c3c4b0 /gn
parentf82b7c5b7ef5bdb9761e48761f683d62d3a05c48 (diff)
parentef781382de7febeec2b4b8f854c88923d9f72e5f (diff)
downloadguix-bioinformatics-c8f84f11abaf1a7945dd704e518a7947136f629b.tar.gz
Merge pull request #6 from Brainiarc7/master
Update this fork with Pjotr's upstream code.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/arrayfire.scm136
-rw-r--r--gn/packages/hyphy.scm105
-rw-r--r--gn/packages/openfyba.scm61
3 files changed, 302 insertions, 0 deletions
diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm
new file mode 100644
index 0000000..23ff0af
--- /dev/null
+++ b/gn/packages/arrayfire.scm
@@ -0,0 +1,136 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
+;;;
+;;; 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 (gn packages arrayfire)
+ #:use-module ((guix licenses))
+ #:use-module (guix download)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system cmake)
+ #:use-module (guix packages)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
+ #:use-module (gnu packages curl)
+ #:use-module (gnu packages gawk)
+ #:use-module (gnu packages cmake)
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages glib)
+ #:use-module (gnu packages image)
+ #:use-module (gnu packages video)
+ #:use-module (gnu packages textutils)
+ #:use-module (gnu packages gl)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages web)
+ #:use-module (gnu packages databases)
+ #:use-module (gnu packages ldc)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages xorg)
+ #:use-module (gnu packages version-control)
+ #:use-module (gnu packages linux))
+
+(define-public arrayfire
+ (package
+ (name "arrayfire")
+ (version "3.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version
+ ".tar.bz2"))
+ (file-name (string-append name "-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "07pbw6vzny3z86y890c0rx7rk31ddchxrrdslk661iq512xppr0g"))))
+ (native-inputs `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("cmake" ,cmake)
+ ("gawk" ,gawk)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs `(("boost" ,boost)
+ ("glfw" ,glfw)
+ ("curl" ,curl)
+ ("dbus" ,dbus)
+ ("enca" ,enca)
+ ("eudev" ,eudev)
+ ("glew" ,glew)
+ ("lapack" ,lapack)
+ ("libcap" ,libcap)
+ ("libjpeg" ,libjpeg)
+ ("libltdl" ,libltdl)
+ ("libtiff" ,libtiff)
+ ("libyajl" ,libyajl)
+ ("mesa-utils" ,mesa-utils)
+ ("mysql" ,mysql)
+ ("python" ,python-2)
+ ("freeimage" ,freeimage)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("fftw-openmpi" ,fftw-openmpi)
+ ("glew" ,glew)
+ ("glu" ,glu)
+ ("openblas" ,openblas)
+ ("git" ,git)
+ ("cmake" ,cmake)))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON") #:tests? #f))
+ (synopsis "ArrayFire: a general purpose GPU library. https://arrayfire.com")
+ (description "ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming simple.")
+ (home-page "http://arrayfire.com/")
+ (license (list gpl2 gpl2+ gpl3 gpl3+))))
+
+(define-public glfw
+ (package
+ (name "glfw")
+ (version "3.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/glfw/glfw/archive/"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika"))))
+ (build-system cmake-build-system)
+ (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") #:tests? #f))
+ (native-inputs `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("cmake" ,cmake)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs `(("curl" ,curl)
+ ("dbus" ,dbus)
+ ("enca" ,enca)
+ ("eudev" ,eudev)
+ ("glew" ,glew)
+ ("libcap" ,libcap)
+ ("libjpeg" ,libjpeg)
+ ("libltdl" ,libltdl)
+ ("libtiff" ,libtiff)
+ ("mesa-utils" ,mesa-utils)
+ ("randrproto" ,randrproto)
+ ("libxrandr" ,libxrandr)
+ ("xineramaproto" ,xineramaproto)
+ ("libxinerama" ,libxinerama)
+ ("libxcursor" ,libxcursor)
+ ("mysql" ,mysql)
+ ("python" ,python-2)))
+ (home-page "http://www.glfw.org/")
+ (synopsis "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.")
+ (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.")
+ (license (list gpl2))))
+
diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm
new file mode 100644
index 0000000..23c0406
--- /dev/null
+++ b/gn/packages/hyphy.scm
@@ -0,0 +1,105 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
+;;;
+;;; 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 (gn packages hyphy)
+ #:use-module ((guix licenses))
+ #:use-module (guix download)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system cmake)
+ #:use-module (guix packages)
+ #:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
+ #:use-module (gnu packages curl)
+ #:use-module (gnu packages gawk)
+ #:use-module (gnu packages cmake)
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages glib)
+ #:use-module (gnu packages image)
+ #:use-module (gnu packages video)
+ #:use-module (gnu packages textutils)
+ #:use-module (gnu packages gl)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages web)
+ #:use-module (gnu packages databases)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages xorg)
+ #:use-module (gnu packages version-control)
+ #:use-module (gnu packages linux))
+
+(define-public hyphy
+ (package
+ (name "hyphy")
+ (version "2.2.6")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/veg/hyphy/archive/" version
+ ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "00i3609nywb1xfq50p3kvfbvahql241ciq23jrf67z0yp4y5l5a9"))))
+ (native-inputs `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("cmake" ,cmake)
+ ("gawk" ,gawk)
+ ("libtool" ,libtool)
+ ("pkg-config" ,pkg-config)))
+ (inputs `(("boost" ,boost)
+ ("curl" ,curl)
+ ("atlas" ,atlas)
+ ("dbus" ,dbus)
+ ("enca" ,enca)
+ ("eudev" ,eudev)
+ ("glew" ,glew)
+ ("lapack" ,lapack)
+ ("libcap" ,libcap)
+ ("libjpeg" ,libjpeg)
+ ("libltdl" ,libltdl)
+ ("libtiff" ,libtiff)
+ ("libyajl" ,libyajl)
+ ("mesa-utils" ,mesa-utils)
+ ("mysql" ,mysql)
+ ("python" ,python-2)
+ ("freeimage" ,freeimage)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("fftw-openmpi" ,fftw-openmpi)
+ ("glew" ,glew)
+ ("glu" ,glu)
+ ("openblas" ,openblas)
+ ("git" ,git)
+ ("cmake" ,cmake)))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:phases (modify-phases %standard-phases
+ (add-after 'unpack `bootstrap
+ (lambda _
+ (zero? (system* "make" "MPI")))))))
+ (arguments
+ `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") #:tests? #f))
+ (synopsis "hyphy: an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.")
+ (description "HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
+ It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for
+ parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as
+ Python and R. ")
+ (home-page "http://hyphy.org")
+ (license (list gpl2 gpl2+ gpl3 gpl3+))))
+
+
+
diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm
new file mode 100644
index 0000000..2b20d09
--- /dev/null
+++ b/gn/packages/openfyba.scm
@@ -0,0 +1,61 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
+;;;
+;;; 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 (gn packages openfyba)
+ #:use-module ((guix licenses))
+ #:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
+ #:use-module (guix packages)
+ #:use-module (guix download)
+ #:use-module (guix build-system gnu)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages textutils)
+ #:use-module (gnu packages base)
+ ;;#:use-module (gnu packages tls)
+ #:use-module (gnu packages zip)
+ #:use-module (gnu packages gnupg)
+ #:use-module (gnu packages bootstrap)
+ #:use-module (guix git-download))
+
+(define-public openfyba
+ (package
+ (name "openfyba")
+ (version "4.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/kartverket/fyba/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ya1agi78d386skq353dk400fl11q6whfqmv31qrkn4g5vamixlr"))))
+ (inputs `(("zip" ,zip)
+ ("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("libgcrypt" ,libgcrypt)))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases (modify-phases %standard-phases
+ (add-after 'unpack `bootstrap
+ (lambda _
+ (zero? (system* "autoreconf" "-vfi")))))))
+ (home-page "http://labs.kartverket.no/sos/")
+ (synopsis "source code release of the FYBA library")
+ (description "OpenFYBA is the source code release of the FYBA library.")
+ (license (list gpl2))))