From 6194045bf42cf551ae1c091b1b353e1ad41c462c Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Sat, 20 Feb 2016 21:28:53 +0300 Subject: Added OpenFYBA library Needed as a dependency to build GDAL, the Geospatial Abstraction Library with support for the Norwegian Data Standard. See https://github.com/kartverket/fyba for more details.--- gn/packages/OpenFYBA | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 gn/packages/OpenFYBA (limited to 'gn') diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA new file mode 100644 index 0000000..378295c --- /dev/null +++ b/gn/packages/OpenFYBA @@ -0,0 +1,59 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Dennis Mungai +;;; +;;; 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 . + +(define-module (gn packages OpenFYBA) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages) + #: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 bootstrap) + #:use-module (guix git-download)) + +(define-public OpenFYBA + (package + (name "OpenFYBA") + (version "4.4.1") + (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 `(("openssl" ,openssl) + (build-system gnu-build-system) + (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, distributed by the +National Mapping Authority of Norway (Statens kartverk) to read and write +files in the National geodata standard format SOSI. +The original library has a long history, and was originally developed for +systems as diverse as DOS, OS/2-16, OS/2-32, Win16, Win32, and various UNIX +variants (POSIX, HPUX, Silicon graphics). In Norwegian. It shows in the +source code. OpenFYBA has been tested to run at least on Windows and Linux +environments. ") + (license license:gpl2+))) + -- cgit v1.2.3 From 98076e5e5fb78118534e399f7fefc68b6b53f151 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 16:47:23 +0300 Subject: Notes: Missing libglw3 build dependencies. To be fixed asap.--- gn/packages/arrayfire.scm | 88 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 gn/packages/arrayfire.scm (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm new file mode 100644 index 0000000..62eceb7 --- /dev/null +++ b/gn/packages/arrayfire.scm @@ -0,0 +1,88 @@ +(define-module (gnu packages arrayfire) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (guix cmake-build-system) + #:use-module (guix licenses) + #: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 tls) + #:use-module (gnu packages textutils) + #:use-module (gnu packages gl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages linux)) + +(define-public arrayfire + (package + (name "arrayfire") + (version "v3.3.alpha") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arrayfire/arrayfire/archive/" version + ".tar.gz")) + (sha256 + (base32 + "0rla0mi5wby8bkpzrj063y6js3d4dlfl3qwfvm8m8skfc21dz52p")))) + (build-system cmake-build-system) + (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("cmake" ,cmake) + ("doxygen" ,doxygen) + ("gawk" ,gawk) + ("gettext" ,gnu-gettext) + ("icedtea7" ,icedtea7) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config) + ("swig" ,swig) + ("which" ,which) + ("yasm" ,yasm))) + (inputs + `(("alsa-lib" ,alsa-lib) + ("boost" ,boost) + ("bzip2" ,bzip2) + ("curl" ,curl) + ("dbus" ,dbus) + ("enca" ,enca) + ("eudev" ,eudev) + ("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("fribidi" ,fribidi) + ("glew" ,glew) + ("gnutls" ,gnutls) + ("gperf" ,gperf) + ("libcap" ,libcap) + ("libcdio" ,libcdio) + ("libgcrypt" ,libgcrypt) + ("libjpeg" ,libjpeg) + ("libltdl" ,libltdl) + ("libssh" ,libssh) + ("libtiff" ,libtiff) + ("libxml2" ,libxml2) + ("libxmu" ,libxmu) + ("libxrandr" ,libxrandr) + ("libxrender" ,libxrender) + ("libxslt" ,libxslt) + ("libxt" ,libxt) + ("libyajl" ,libyajl) + ("lzo" ,lzo) + ("mesa-utils" ,mesa-utils) + ("mysql" ,mysql) + ("openssl" ,openssl) + ("pcre" ,pcre) + ("python" ,python-2) + ("tinyxml" ,tinyxml) + ("unzip" ,unzip) + ("zip" ,zip) + ("zlib" ,zlib))) + (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 gpl3+))) -- cgit v1.2.3 From de91415e4712df24902ff80b550d85fbb6c59381 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:06:06 +0300 Subject: Added GFWL as a build dependency *BOOM*--- gn/packages/arrayfire.scm | 63 ++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 60 insertions(+), 3 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 62eceb7..9896baf 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -45,8 +45,7 @@ ("which" ,which) ("yasm" ,yasm))) (inputs - `(("alsa-lib" ,alsa-lib) - ("boost" ,boost) + `(("boost" ,boost) ("bzip2" ,bzip2) ("curl" ,curl) ("dbus" ,dbus) @@ -59,7 +58,6 @@ ("gnutls" ,gnutls) ("gperf" ,gperf) ("libcap" ,libcap) - ("libcdio" ,libcdio) ("libgcrypt" ,libgcrypt) ("libjpeg" ,libjpeg) ("libltdl" ,libltdl) @@ -86,3 +84,62 @@ (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 gpl3+))) + +(define-public glfw + (package + (name "glfw") + (version "3.0.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/glfw/glfw/archive/" + version ".zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "0njplyalwwqh7xr7xc7klc6x06mq0ak8w2pxh85w8n4hxkmqqnf5")))) + (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("cmake" ,cmake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("bzip2" ,bzip2) + ("curl" ,curl) + ("dbus" ,dbus) + ("enca" ,enca) + ("eudev" ,eudev) + ("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("fribidi" ,fribidi) + ("glew" ,glew) + ("gnutls" ,gnutls) + ("gperf" ,gperf) + ("libcap" ,libcap) + ("libgcrypt" ,libgcrypt) + ("libjpeg" ,libjpeg) + ("libltdl" ,libltdl) + ("libssh" ,libssh) + ("libtiff" ,libtiff) + ("libxml2" ,libxml2) + ("libxmu" ,libxmu) + ("libxrandr" ,libxrandr) + ("libxrender" ,libxrender) + ("libxslt" ,libxslt) + ("libxt" ,libxt) + ("lzo" ,lzo) + ("mesa-utils" ,mesa-utils) + ("mysql" ,mysql) + ("openssl" ,openssl) + ("python" ,python-2) + ("tinyxml" ,tinyxml) + ("unzip" ,unzip) + ("zip" ,zip) + ("zlib" ,zlib))) + (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. It is easy to integrate into existing applications and does not lay claim to the main loop. +GLFW is written in C and has native support for Windows, OS X and many Unix-like systems using the X Window System, such as Linux and FreeBSD. +GLFW is licensed under the zlib/libpng license.") + (license license:gpl2+))) -- cgit v1.2.3 From 92905620b39f86181e6d684cc43df7758a6ffeb7 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:08:01 +0300 Subject: Added Licensing information. Licensing, do you speak it?--- gn/packages/arrayfire.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 9896baf..75de462 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -1,3 +1,21 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Dennis Mungai +;;; +;;; 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 . + (define-module (gnu packages arrayfire) #:use-module (guix packages) #:use-module (guix download) -- cgit v1.2.3 From 6a2a970193719fd3064da1fc6c3cd68547d28f17 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:11:21 +0300 Subject: Fix the hash of glfw, based on sha256sum Bad hash, no build, mate.--- gn/packages/arrayfire.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 75de462..128d79b 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -114,7 +114,7 @@ (file-name (string-append name "-" version ".zip")) (sha256 (base32 - "0njplyalwwqh7xr7xc7klc6x06mq0ak8w2pxh85w8n4hxkmqqnf5")))) + "1g0jm80cakk60477zz9z1mpsznxaadsfm318yiigf6kackrkqfqg")))) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) (native-inputs `(("autoconf" ,autoconf) -- cgit v1.2.3 From 20fab34390b8d8716cf2ca21e650eefbc86eb4de Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:12:26 +0300 Subject: Declared package as a GNU Guix package. See gnu packages definition at the beginning.--- gn/packages/OpenFYBA | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA index 378295c..5d64381 100644 --- a/gn/packages/OpenFYBA +++ b/gn/packages/OpenFYBA @@ -16,7 +16,7 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . -(define-module (gn packages OpenFYBA) +(define-module (gnu packages OpenFYBA) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (guix packages) -- cgit v1.2.3 From 003dc6dfd82f61bfadf595058dfd6f1213b6ca4a Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:15:25 +0300 Subject: Add glfw as an input to arrayfire's build. See the inputs section entry at ("glfw" ,glfw)--- gn/packages/arrayfire.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 128d79b..6f326c9 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -65,6 +65,7 @@ (inputs `(("boost" ,boost) ("bzip2" ,bzip2) + ("glfw" ,glfw) ("curl" ,curl) ("dbus" ,dbus) ("enca" ,enca) -- cgit v1.2.3 From b70b4572ebf97d83296b8bfd11263f07b1f385a3 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:37:00 +0300 Subject: Add fftw-openmpi as build dependencies. Needed to build a running binary.--- gn/packages/arrayfire.scm | 9 +++++++++ 1 file changed, 9 insertions(+) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 6f326c9..4f4e004 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -32,6 +32,9 @@ #:use-module (gnu packages video) #:use-module (gnu packages tls) #:use-module (gnu packages textutils) + #:use-module (gnu packages fftw) + #:use-module (gnu packages fftw-openmpi) + #:use-module (gnu packages fftwf) #:use-module (gnu packages gl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages linux)) @@ -98,6 +101,12 @@ ("tinyxml" ,tinyxml) ("unzip" ,unzip) ("zip" ,zip) + ("freeimage" ,freeimage) + ("fftw" ,fftw) + ("fftwf" ,fftwf) + ("fftw-openmpi" ,fftw-openmpi) + ("atlas" ,atlas) + ("gfortran", gfortran) ("zlib" ,zlib))) (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.") -- cgit v1.2.3 From a83c940bddf3be8dd041c00b989785e9ffe8891b Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:47:59 +0300 Subject: Added essential headers. I commit to master directly. Needed: OpenCL headers. Challenge accepted.--- gn/packages/arrayfire.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 4f4e004..b517917 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -36,7 +36,9 @@ #:use-module (gnu packages fftw-openmpi) #:use-module (gnu packages fftwf) #:use-module (gnu packages gl) + #:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages mesa) #:use-module (gnu packages linux)) (define-public arrayfire @@ -107,6 +109,14 @@ ("fftw-openmpi" ,fftw-openmpi) ("atlas" ,atlas) ("gfortran", gfortran) + ("glew" ,glew) + ("glu" ,glu) + ("libx11" ,libx11) + ("libxi" ,libxi) + ("libxrandr" ,libxrandr) + ("libxxf86vm" ,libxxf86vm) + ("inputproto" ,inputproto) + ("glproto" ,glproto) ("zlib" ,zlib))) (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.") -- cgit v1.2.3 From 5fa516d92634ac957d276330b5795416cffdc566 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Tue, 23 Feb 2016 17:52:53 +0300 Subject: Khronos OpenCL headers still needed. The burn is strong on this one.--- gn/packages/arrayfire.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index b517917..1d3401d 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) #:use-module (gnu packages mesa) + #:use-module (gnu packages web) #:use-module (gnu packages linux)) (define-public arrayfire -- cgit v1.2.3 From 362952ac8741a7f44b8176de3e7b15fbb8fae0b1 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 09:28:24 +0000 Subject: Add older version of python-pil --- gn/packages/python.scm | 86 +++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 71 insertions(+), 15 deletions(-) (limited to 'gn') diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 8f2bc80..61d186b 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -357,23 +357,79 @@ project)") (description #f) (license #f))) -(define-public python2-piddle +(define-public python2-pil-1.1.6 (package - (name "python2-piddle") - (version "1.0.15") + (name "python2-pil") + (version "1.1.6") (source - (origin - (method url-fetch) - (uri (string-append - ;; http://sourceforge.net/projects/numpy/files/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz/download - "mirror://sourceforge/piddle/piddle-" version ".zip" - )) - ;; (file-name (string-append name "-" version ".zip")) - (sha256 - (base32 - "0jaxfsrcgqb5cf2wznxnpdws5khlrdixmg85lrhq2zl9cy6dfdya")))) - (native-inputs - `(("unzip" ,unzip))) + (origin + (method url-fetch) + (uri (string-append + "http://effbot.org/downloads/Imaging-" + version ".tar.gz")) + (sha256 + (base32 + "141zidl3s9v4vfi3nsbg42iq1lc2a932gprqr1kij5hrnn53bmvx")) + (modules '((guix build utils))) + (snippet + ;; Adapt to newer freetype. As the package is unmaintained upstream, + ;; there is no use in creating a patch and reporting it. + '(substitute* "_imagingft.c" + (("freetype/") + "freetype2/"))))) + (build-system python-build-system) + (inputs + `(("freetype" ,freetype) + ("libjpeg" ,libjpeg) + ("libtiff" ,libtiff) + ("python-setuptools" ,python-setuptools) + ("zlib" ,zlib))) + (arguments + ;; Only the fork python-pillow works with Python 3. + `(#:python ,python-2 + #:tests? #f ; no check target + #:phases + (alist-cons-before + 'build 'configure + ;; According to README and setup.py, manual configuration is + ;; the preferred way of "searching" for inputs. + ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter. + (lambda* (#:key inputs #:allow-other-keys) + (let ((jpeg (assoc-ref inputs "libjpeg")) + (zlib (assoc-ref inputs "zlib")) + (tiff (assoc-ref inputs "libtiff")) + (freetype (assoc-ref inputs "freetype"))) + (substitute* "setup.py" + (("JPEG_ROOT = None") + (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")")) + (("ZLIB_ROOT = None") + (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")")) + (("TIFF_ROOT = None") + (string-append "TIFF_ROOT = libinclude(\"" tiff "\")")) + (("FREETYPE_ROOT = None") + (string-append "FREETYPE_ROOT = libinclude(\"" + freetype "\")"))))) + %standard-phases))) + (home-page "http://www.pythonware.com/products/pil/") + (synopsis "Python Imaging Library") + (description "The Python Imaging Library (PIL) adds image processing +capabilities to the Python interpreter.") + (license (license:x11-style + "file://README" + "See 'README' in the distribution.")))) + +(define-public python2-piddle-gn + (package + (name "python2-piddle") + (version "1.0.15-gn") + (source (origin + (method url-fetch) + (uri (string-append + "http://files.genenetwork.org/software/contrib/piddle-" +version "-gn.tgz")) + (sha256 + (base32 + "0yl6frmhy94cmwzdks7ndc7nzh1ml2a4ch86gz2l7wcwpxjhwgmk")))) (build-system python-build-system) ;; (native-inputs -- cgit v1.2.3 From 0660647c4bf43114a087337fa11131313afc7b9a Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 09:29:13 +0000 Subject: Small GN database --- gn/packages/genenetwork.scm | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2f755a6..dea6eae 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -178,7 +178,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) + ("python2-piddle-gn2" ,python2-piddle-gn2) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) @@ -202,3 +202,35 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x + +(define-public genenetwork2-database-small + (let ((md5 "93e745e9c")) + (package + (name "genenetwork2-database-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") + (file-name (string-append name "-" md5)) + (sha256 + (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) + (build-system trivial-build-system) + (native-inputs `(("unzip" ,unzip) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) + ) + (and (mkdir "db") + (zero? (system* unzip source "-d" "db")) + (chdir "db")))))) + (home-page "http://genenetwork.org/") + (synopsis "Small database to run on genenetwork") + (description "Genenetwork installation + database.") + (license license:agpl3+)))) + -- cgit v1.2.3 From 8c2f2f7f65441a3b66bc2d9b145cd9065461d0cc Mon Sep 17 00:00:00 2001 From: pjotrp Date: Thu, 25 Feb 2016 11:02:28 +0000 Subject: Fix python-piddle --- gn/packages/genenetwork.scm | 2 +- gn/packages/python.scm | 17 +++++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) (limited to 'gn') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index dea6eae..b77ccb4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -178,7 +178,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle-gn2" ,python2-piddle-gn2) + ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 61d186b..7781521 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -426,19 +426,20 @@ capabilities to the Python interpreter.") (method url-fetch) (uri (string-append "http://files.genenetwork.org/software/contrib/piddle-" -version "-gn.tgz")) +version ".tgz")) (sha256 (base32 - "0yl6frmhy94cmwzdks7ndc7nzh1ml2a4ch86gz2l7wcwpxjhwgmk")))) + "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq")))) (build-system python-build-system) - ;; (native-inputs - ;; `(("python-setuptools" ,python-setuptools))) + (native-inputs + `(("python2-setuptools" ,python2-setuptools))) (arguments - `(#:python ,python-2 - #:tests? #f - )) ; no 'setup.py test' really! - (home-page "http://www.numpy.org/") + `( + #:python ,python-2 + #:tests? #f ; no 'setup.py test' really! + )) + (home-page #f) (synopsis "Canvas drawing library for python2 (old!)") (description #f) (license #f))) -- cgit v1.2.3 From 859709f054229f45eba23d1e3c58e6b3037c2172 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Thu, 25 Feb 2016 19:58:41 +0300 Subject: Applied Pjotr's patch. Applied Pjotr's patch.--- gn/packages/arrayfire.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 1d3401d..5869a88 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -16,12 +16,13 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . -(define-module (gnu packages arrayfire) +(define-module (gn packages arrayfire) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) - #:use-module (guix cmake-build-system) + #:use-module (guix build-system cmake) #:use-module (guix licenses) + #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages curl) #:use-module (gnu packages gawk) @@ -32,9 +33,9 @@ #:use-module (gnu packages video) #:use-module (gnu packages tls) #:use-module (gnu packages textutils) - #:use-module (gnu packages fftw) - #:use-module (gnu packages fftw-openmpi) - #:use-module (gnu packages fftwf) + ;; #:use-module (gnu packages fftw) + ;; #:use-module (gnu packages fftw-openmpi) - in algebra + ;; #:use-module (gnu packages fftwf) #:use-module (gnu packages gl) #:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) -- cgit v1.2.3 From 61435b2d111793806f19793655a3a187aec9562e Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 26 Feb 2016 08:43:13 +0000 Subject: Fix ruby error --- gn/packages/ruby.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index 0e1fa88..bebc678 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -16,7 +16,7 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . -(define-module (gnu packages ruby) +(define-module (gn packages ruby) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages compression) -- cgit v1.2.3 From b7db2ef030ce2c0845c172f8da27954f5c7a4fbf Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 10:41:19 +0000 Subject: Restarted r-wgcna --- gn/packages/bioinformatics.scm | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index bf39935..7b96604 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -61,23 +61,24 @@ "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) - ;; (propagated-inputs - ;; `( ;; ("r-annotationdbi" ,r-annotationdbi) - ;; ("r-doparallel" ,r-doparallel) - ;; ("r-dynamictreecut" ,r-dynamictreecut) - ;; ("r-fastcluster" ,r-fastcluster) - ;; ("r-foreach" ,r-foreach) - ;; ("r-go.db" ,r-go.db) - ;; ("r-grdevices" ,r-grdevices) - ;; ("r-hmisc" ,r-hmisc) - ;; ("r-impute" ,r-impute) - ;; ("r-matrixstats" ,r-matrixstats) - ;; ("r-parallel" ,r-parallel) - ;; ("r-preprocesscore" ,r-preprocesscore) - ;; ("r-splines" ,r-splines) - ;; ("r-stats" ,r-stats) - ;; ("r-survival" ,r-survival) - ;; ("r-utils" ,r-utils))) + (propagated-inputs + `( ;; ("r-annotationdbi" ,r-annotationdbi) + ("r-biocparallel" ,r-biocparallel) + ; ("r-dynamictreecut" ,r-dynamictreecut) + ; ("r-fastcluster" ,r-fastcluster) + ; ("r-foreach" ,r-foreach) + ("r-go-db" ,r-go-db) + ; ("r-grdevices" ,r-grdevices) + ; ("r-hmisc" ,r-hmisc) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ; ("r-parallel" ,r-parallel) + ; ("r-preprocesscore" ,r-preprocesscore) + ; ("r-splines" ,r-splines) + ; ("r-stats" ,r-stats) + ; ("r-survival" ,r-survival) + ; ("r-utils" ,r-utils) + )) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis -- cgit v1.2.3 From 182c7797cc905faa1a2d497397ef465bbf484ca2 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 10:41:49 +0000 Subject: rdmd has moved into guix proper --- gn/packages/bioinformatics.scm | 42 ------------------------------------------ 1 file changed, 42 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 7b96604..405e5b3 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -269,48 +269,6 @@ mixed model and some of its close relatives for genome-wide association studies (GWAS).") (license license:gpl3)))) -(define-public rdmd - (let ((commit "4dba6877c")) - (package - (name "rdmd") - (version "20160217") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/D-Programming-Language/tools.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45")))) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) ; There is no Makefile, so there's no 'make check'. - (replace - 'build - (lambda _ - (zero? (system* "ldc2" "rdmd.d")))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) - (copy-file "rdmd" (string-append bin "/rdmd")))))))) - (native-inputs - `(("ldc" ,ldc))) - (home-page "https://github.com/D-Programming-Language/tools/") - (synopsis "Tool for the D language which is used for compiling") - (description - "rdmd is a companion to the dmd compiler that simplifies the typical -edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like -make and other tools, rdmd uses the relative dates of the files involved to -minimize the amount of work necessary. Unlike make, rdmd tracks dependencies -and freshness without requiring additional information from the user.") - (license license:boost1.0)))) - (define-public sambamba (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) (package -- cgit v1.2.3 From 42d110f144f36f6b1bf2092254ca3286094bb206 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 11:18:38 +0000 Subject: r-wgca: git fetch --- gn/packages/bioinformatics.scm | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 405e5b3..2bdf47a 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -49,25 +49,28 @@ #:use-module (srfi srfi-1)) (define-public r-wgcna + (let ((commit "9c68667c3")) (package (name "r-wgcna") - (version "1.48") - (source - (origin - (method url-fetch) - (uri (cran-uri "WGCNA" version)) - (sha256 - (base32 - "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn")))) + (version (string-append "1.49-" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/WGCNA.git") + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf581")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs `( ;; ("r-annotationdbi" ,r-annotationdbi) - ("r-biocparallel" ,r-biocparallel) + ; ("r-biocparallel" ,r-biocparallel) ; ("r-dynamictreecut" ,r-dynamictreecut) ; ("r-fastcluster" ,r-fastcluster) ; ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) + ; ("r-go-db" ,r-go-db) ; ("r-grdevices" ,r-grdevices) ; ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) @@ -85,7 +88,7 @@ "Weighted Correlation Network Analysis") (description "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.") - (license license:gpl2+))) + (license license:gpl2+)))) (define-public qtlreaper (package -- cgit v1.2.3 From d5a9e7dd0616461ec9960b9e57665dcc766d9b33 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 11:48:50 +0000 Subject: r-wgcna deps --- gn/packages/bioinformatics.scm | 24 +++++++----- gn/packages/statistics.scm | 85 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 100 insertions(+), 9 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2bdf47a..dd7e77e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -49,27 +49,28 @@ #:use-module (srfi srfi-1)) (define-public r-wgcna - (let ((commit "9c68667c3")) + (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49")) (package (name "r-wgcna") (version (string-append "1.49-" commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/genenetwork/WGCNA.git") + ;; (url "https://github.com/genenetwork/WGCNA.git") + (url "https://github.com/pjotrp/WGCNA.git") (commit commit))) (file-name (string-append name "-" commit)) (sha256 (base32 - "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf581")))) + "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs `( ;; ("r-annotationdbi" ,r-annotationdbi) ; ("r-biocparallel" ,r-biocparallel) - ; ("r-dynamictreecut" ,r-dynamictreecut) - ; ("r-fastcluster" ,r-fastcluster) - ; ("r-foreach" ,r-foreach) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-fastcluster" ,r-fastcluster) + ("r-foreach" ,r-foreach) ; ("r-go-db" ,r-go-db) ; ("r-grdevices" ,r-grdevices) ; ("r-hmisc" ,r-hmisc) @@ -85,9 +86,14 @@ (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis - "Weighted Correlation Network Analysis") + "Weighted gene correlation network analysis (wgcna)") (description - "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.") + "Functions necessary to perform Weighted Correlation Network +Analysis on high-dimensional data. Includes functions for rudimentary +data cleaning, construction of correlation networks, module +identification, summarization, and relating of variables and modules +to sample traits. Also includes a number of utility functions for +data manipulation and visualization.") (license license:gpl2+)))) (define-public qtlreaper @@ -123,7 +129,7 @@ test. For the permutation test, it performs only as many permutations as are necessary to define the empirical P-value to a reasonable precision. It also performs bootstrap resampling to estimate the confidence region for the location of a putative QTL.") - (license license:gpl2))) + (license license:gpl2+))) (define-public plink2 (package diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index 2d83816..57ddfe6 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -39,6 +39,91 @@ #:use-module (gnu packages bootstrap) #:use-module (srfi srfi-1)) +(define-public r-iterators +(package + (name "r-iterators") + (version "1.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "iterators" version)) + (sha256 + (base32 + "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf")))) + (build-system r-build-system) + ;; (propagated-inputs `(("r-utils" ,r-utils))) + (home-page + "http://cran.r-project.org/web/packages/iterators") + (synopsis "Provides Iterator Construct for R") + (description + "Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.") + (license #f))) + +(define-public r-foreach +(package + (name "r-foreach") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "foreach" version)) + (sha256 + (base32 + "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y")))) + (build-system r-build-system) + (propagated-inputs `(("r-iterators" ,r-iterators))) + (home-page + "http://cran.r-project.org/web/packages/foreach") + (synopsis + "Provides Foreach Looping Construct for R") + (description + "Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.") + (license #f)) +) + +(define-public r-fastcluster +(package + (name "r-fastcluster") + (version "1.1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastcluster" version)) + (sha256 + (base32 + "0x2prrsnqi5iqx23ki6y2agndjq8058ph6s703i4avrqi1q1w1q8")))) + (build-system r-build-system) + (home-page + "http://danifold.net/fastcluster.html") + (synopsis + "Fast Hierarchical Clustering Routines for R and Python") + (description + "This is a two-in-one package which provides interfaces to both R and Python. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: \"linkage\" in the SciPy package \"scipy.cluster.hierarchy\", \"hclust\" in R's \"stats\" package, and the \"flashClust\" package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the Python files, see the file INSTALL in the source distribution.") + (license #f))) + +(define-public r-dynamictreecut +(package + (name "r-dynamictreecut") + (version "1.62") + (source + (origin + (method url-fetch) + (uri (cran-uri "dynamicTreeCut" version)) + (sha256 + (base32 + "1y11gg6k32wpsyb10kdv176ivczx2jlizs1xsrjrs6iwbncwzrkp")))) + (properties + `((upstream-name . "dynamicTreeCut"))) + (build-system r-build-system) + ; (propagated-inputs `(("r-stats" ,r-stats))) + (home-page + "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/") + (synopsis + "Methods for detection of clusters in hierarchical clustering dendrograms.") + (description + "Contains methods for detection of clusters in hierarchical clustering dendrograms.") + (license license:gpl2+))) + (define-public r-rcppeigen (package (name "r-rcppeigen") -- cgit v1.2.3 From 71684ab0577b60b53d4a459e97bb5540952ea4d9 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 12:45:40 +0000 Subject: r-wgcna deps --- gn/packages/bioinformatics.scm | 12 ++++-- gn/packages/statistics.scm | 85 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 93 insertions(+), 4 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index dd7e77e..92be2b4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -49,7 +49,7 @@ #:use-module (srfi srfi-1)) (define-public r-wgcna - (let ((commit "41b24edb522a200b671e8e25f6ffb67769113a49")) + (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) (package (name "r-wgcna") (version (string-append "1.49-" commit)) @@ -62,18 +62,19 @@ (file-name (string-append name "-" commit)) (sha256 (base32 - "1ad2lgdz8dy8imn4my83jz4xqp4m3phyakfssmdjcp362g739p2w")))) + "1zqnsb8s3065rq1y2y3l79zi8wmdwjkcjls96ypycrb7pmdil58j")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs `( ;; ("r-annotationdbi" ,r-annotationdbi) ; ("r-biocparallel" ,r-biocparallel) ("r-dynamictreecut" ,r-dynamictreecut) + ("r-doparallel" ,r-doparallel) ("r-fastcluster" ,r-fastcluster) ("r-foreach" ,r-foreach) - ; ("r-go-db" ,r-go-db) + ("r-go-db" ,r-go-db) ; ("r-grdevices" ,r-grdevices) - ; ("r-hmisc" ,r-hmisc) + ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) ("r-matrixstats" ,r-matrixstats) ; ("r-parallel" ,r-parallel) @@ -83,6 +84,9 @@ ; ("r-survival" ,r-survival) ; ("r-utils" ,r-utils) )) + (arguments + `( + #:tests? #f)) ; no 'setup.py test' (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index 57ddfe6..cc2726c 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -18,6 +18,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages cpio) #:use-module (gnu packages file) + #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) @@ -39,6 +40,90 @@ #:use-module (gnu packages bootstrap) #:use-module (srfi srfi-1)) +(define-public r-acepack +(package + (name "r-acepack") + (version "1.3-3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acepack" version)) + (sha256 + (base32 + "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page + "http://cran.r-project.org/web/packages/acepack") + (synopsis + "ace() and avas() for selecting regression transformations") + (description + "ACE and AVAS methods for choosing regression transformations.") + (license license:x11))) + +(define-public r-hmisc +(package + (name "r-hmisc") + (version "3.17-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Hmisc" version)) + (sha256 + (base32 + "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg")))) + (properties `((upstream-name . "Hmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-acepack" ,r-acepack) + ; ("r-cluster" ,r-cluster) + ; ("r-foreign" ,r-foreign) + ; ("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ; ("r-grid" ,r-grid) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-lattice" ,r-lattice) + ; ("r-latticeextra" ,r-latticeextra) + ; ("r-methods" ,r-methods) + ; ("r-nnet" ,r-nnet) + ; ("r-rpart" ,r-rpart) + ; ("r-survival" ,r-survival))) + )) + (home-page + "http://biostat.mc.vanderbilt.edu/Hmisc") + (synopsis "Harrell Miscellaneous") + (description + "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.") + (license license:gpl2+))) + +(define-public r-doparallel +(package + (name "r-doparallel") + (version "1.0.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "doParallel" version)) + (sha256 + (base32 + "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh")))) + (properties `((upstream-name . "doParallel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ;; ("r-parallel" ,r-parallel) + )) + (home-page + "http://cran.r-project.org/web/packages/doParallel") + (synopsis + "Foreach Parallel Adaptor for the 'parallel' Package") + (description + "Provides a parallel backend for the %dopar% function using the parallel package.") + (license license:gpl2+))) + (define-public r-iterators (package (name "r-iterators") -- cgit v1.2.3 From b280af1638843cc3b3ca14933a07b66076b0713d Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 13:03:03 +0000 Subject: r-wgcna deps --- gn/packages/statistics.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 54 insertions(+), 2 deletions(-) (limited to 'gn') diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index cc2726c..2c9ebda 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -62,6 +62,54 @@ "ACE and AVAS methods for choosing regression transformations.") (license license:x11))) +(define-public r-latticeextra +(package + (name "r-latticeextra") + (version "0.6-28") + (source + (origin + (method url-fetch) + (uri (cran-uri "latticeExtra" version)) + (sha256 + (base32 + "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) + (properties `((upstream-name . "latticeExtra"))) + (build-system r-build-system) + (propagated-inputs + `( ;;("r-grdevices" ,r-grdevices) + ("r-gridbase" ,r-gridbase) + ("r-lattice" ,r-lattice) + ("r-rcolorbrewer" ,r-rcolorbrewer) + )) + (home-page + "http://latticeextra.r-forge.r-project.org/") + (synopsis + "Extra Graphical Utilities Based on Lattice") + (description + "Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.") + (license license:gpl2+))) + +(define-public r-formula + (package + (name "r-formula") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Formula" version)) + (sha256 + (base32 + "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) + (properties `((upstream-name . "Formula"))) + (build-system r-build-system) + (home-page + "http://cran.r-project.org/web/packages/Formula") + (synopsis "Extended Model Formulas") + (description + "Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.") + (license #f)) +) + (define-public r-hmisc (package (name "r-hmisc") @@ -75,17 +123,21 @@ "110w5hbrl10isslqs0iq6w2ll0dafqyqznb50cdcallnlnvbvxrg")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (arguments + `(#:tests? #f)) ; no 'setup.py test' (propagated-inputs `(("r-acepack" ,r-acepack) ; ("r-cluster" ,r-cluster) ; ("r-foreign" ,r-foreign) - ; ("r-formula" ,r-formula) + ("r-formula" ,r-formula) ("r-ggplot2" ,r-ggplot2) ; ("r-grid" ,r-grid) ("r-gridextra" ,r-gridextra) ("r-gtable" ,r-gtable) ("r-lattice" ,r-lattice) - ; ("r-latticeextra" ,r-latticeextra) + ("r-latticeextra" ,r-latticeextra) ; ("r-methods" ,r-methods) ; ("r-nnet" ,r-nnet) ; ("r-rpart" ,r-rpart) -- cgit v1.2.3 From f82b7c5b7ef5bdb9761e48761f683d62d3a05c48 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sun, 28 Feb 2016 17:42:06 +0000 Subject: r-wgcna deps --- gn/packages/bioinformatics.scm | 24 +++++++++++++++++++++++- gn/packages/genenetwork.scm | 1 + 2 files changed, 24 insertions(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 92be2b4..b503e22 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -48,6 +48,28 @@ #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) + +(define-public r-biocpreprocesscore + (package + (name "r-biocpreprocesscore") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "preprocessCore" version)) + (sha256 + (base32 + "07isghjkqm91rg37l1fzpjrbq36b7w4pbsi95wwh6a8qq7r69z1n")))) + (properties + `((upstream-name . "BiocpreprocessCore") + (r-repository . bioconductor))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/preprocessCore") + (synopsis "Preprocess functions for Bioconductor") + (description + "A library of core preprocessing routines.") + (license license:lgpl2.0+))) + + (define-public r-wgcna (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb")) (package @@ -78,7 +100,7 @@ ("r-impute" ,r-impute) ("r-matrixstats" ,r-matrixstats) ; ("r-parallel" ,r-parallel) - ; ("r-preprocesscore" ,r-preprocesscore) + ("r-biocpreprocesscore" ,r-biocpreprocesscore) ; ("r-splines" ,r-splines) ; ("r-stats" ,r-stats) ; ("r-survival" ,r-survival) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index b77ccb4..033bf94 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -158,6 +158,7 @@ (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) + ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) -- cgit v1.2.3 From c4a22933adfe218e991715a1c1e25d2104c48900 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Sun, 28 Feb 2016 21:37:32 +0300 Subject: Lisp specific fixes. --- gn/packages/arrayfire.scm | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 5869a88..e529971 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -17,7 +17,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gn packages arrayfire) - #:use-module (guix packages) + #:use-module ((guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) @@ -33,15 +33,12 @@ #:use-module (gnu packages video) #:use-module (gnu packages tls) #:use-module (gnu packages textutils) - ;; #:use-module (gnu packages fftw) - ;; #:use-module (gnu packages fftw-openmpi) - in algebra - ;; #:use-module (gnu packages fftwf) #:use-module (gnu packages gl) #:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) #:use-module (gnu packages mesa) #:use-module (gnu packages web) - #:use-module (gnu packages linux)) + #:use-module (gnu packages linux))) (define-public arrayfire (package @@ -51,11 +48,13 @@ (method url-fetch) (uri (string-append "https://github.com/arrayfire/arrayfire/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0rla0mi5wby8bkpzrj063y6js3d4dlfl3qwfvm8m8skfc21dz52p")))) (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) + (arguments + `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -179,7 +178,6 @@ ("zlib" ,zlib))) (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. It is easy to integrate into existing applications and does not lay claim to the main loop. -GLFW is written in C and has native support for Windows, OS X and many Unix-like systems using the X Window System, such as Linux and FreeBSD. -GLFW is licensed under the zlib/libpng license.") + (description "glfw is an Open Source, multi-platform library for creating windows with OpenGL contexts and receiving input and events.") (license license:gpl2+))) + -- cgit v1.2.3 From 0e91d686b2262bf19b15aa64477daad08ae94926 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Sun, 28 Feb 2016 22:42:45 +0300 Subject: Lisp fixes --- gn/packages/arrayfire.scm | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index e529971..c82ed5c 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -17,7 +17,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gn packages arrayfire) - #:use-module ((guix packages) + #:use-module ((guix packages)) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) @@ -31,14 +31,15 @@ #:use-module (gnu packages glib) #:use-module (gnu packages image) #:use-module (gnu packages video) - #:use-module (gnu packages tls) + ;;#:use-module (gnu packages tls) #:use-module (gnu packages textutils) #:use-module (gnu packages gl) - #:use-module (gnu packages glew) + ;;#:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages mesa) + ;;#:use-module (gnu packages mesa) #:use-module (gnu packages web) - #:use-module (gnu packages linux))) + #:use-module (gnu packages ldc) + #:use-module (gnu packages linux)) (define-public arrayfire (package @@ -52,11 +53,7 @@ (sha256 (base32 "0rla0mi5wby8bkpzrj063y6js3d4dlfl3qwfvm8m8skfc21dz52p")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) - (native-inputs - `(("autoconf" ,autoconf) + (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) ("doxygen" ,doxygen) @@ -68,8 +65,7 @@ ("swig" ,swig) ("which" ,which) ("yasm" ,yasm))) - (inputs - `(("boost" ,boost) + (inputs `(("boost" ,boost) ("bzip2" ,bzip2) ("glfw" ,glfw) ("curl" ,curl) @@ -118,7 +114,12 @@ ("libxxf86vm" ,libxxf86vm) ("inputproto" ,inputproto) ("glproto" ,glproto) + ("cmake" ,cmake) ("zlib" ,zlib))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) + (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/") @@ -176,6 +177,7 @@ ("unzip" ,unzip) ("zip" ,zip) ("zlib" ,zlib))) + (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.") -- cgit v1.2.3 From 5336d44d8727f938aaf913861de4835c0793eac9 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Sun, 28 Feb 2016 23:19:54 +0300 Subject: Update arrayfire.scm --- gn/packages/arrayfire.scm | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index c82ed5c..e09fff8 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -17,11 +17,11 @@ ;;; along with GNU Guix. If not, see . (define-module (gn packages arrayfire) - #:use-module ((guix packages)) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) - #:use-module (guix licenses) + #:use-module (guix packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages curl) @@ -118,12 +118,11 @@ ("zlib" ,zlib))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) - + `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) (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 gpl3+))) + (license gpl2+))) (define-public glfw (package @@ -138,14 +137,12 @@ (base32 "1g0jm80cakk60477zz9z1mpsznxaadsfm318yiigf6kackrkqfqg")))) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) - (native-inputs - `(("autoconf" ,autoconf) + (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) - (inputs - `(("bzip2" ,bzip2) + (inputs `(("bzip2" ,bzip2) ("curl" ,curl) ("dbus" ,dbus) ("enca" ,enca) @@ -176,10 +173,9 @@ ("tinyxml" ,tinyxml) ("unzip" ,unzip) ("zip" ,zip) - ("zlib" ,zlib))) - + ("zlib" ,zlib))) (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 license:gpl2+))) + (license gpl2))) -- cgit v1.2.3 From 2814c72f084f175bbc7cfc401ea59662f1595596 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 01:48:00 +0300 Subject: Pending work: Fix Licensing stuff. The build should run, though you'll run into bigger problems with licensing.--- gn/packages/arrayfire.scm | 66 ++++++++--------------------------------------- 1 file changed, 11 insertions(+), 55 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index e09fff8..3244680 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -17,7 +17,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gn packages arrayfire) - #:use-module ((guix licenses) #:prefix license:) + #:use-module ((guix licenses)) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) @@ -38,7 +38,11 @@ #:use-module (gnu packages pkg-config) ;;#:use-module (gnu packages mesa) #:use-module (gnu packages web) + #:use-module (gnu packages databases) + ;;#:use-module (gnu packages lapack) #:use-module (gnu packages ldc) + ;;#:use-module (gnu packages gfortran) + #:use-module (gnu packages python) #:use-module (gnu packages linux)) (define-public arrayfire @@ -56,64 +60,32 @@ (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) - ("doxygen" ,doxygen) ("gawk" ,gawk) - ("gettext" ,gnu-gettext) - ("icedtea7" ,icedtea7) ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("swig" ,swig) - ("which" ,which) - ("yasm" ,yasm))) + ("pkg-config" ,pkg-config))) (inputs `(("boost" ,boost) - ("bzip2" ,bzip2) ("glfw" ,glfw) ("curl" ,curl) ("dbus" ,dbus) ("enca" ,enca) ("eudev" ,eudev) - ("fontconfig" ,fontconfig) ("freetype" ,freetype) - ("fribidi" ,fribidi) ("glew" ,glew) - ("gnutls" ,gnutls) - ("gperf" ,gperf) ("libcap" ,libcap) - ("libgcrypt" ,libgcrypt) ("libjpeg" ,libjpeg) ("libltdl" ,libltdl) - ("libssh" ,libssh) ("libtiff" ,libtiff) - ("libxml2" ,libxml2) - ("libxmu" ,libxmu) - ("libxrandr" ,libxrandr) - ("libxrender" ,libxrender) - ("libxslt" ,libxslt) - ("libxt" ,libxt) ("libyajl" ,libyajl) - ("lzo" ,lzo) ("mesa-utils" ,mesa-utils) ("mysql" ,mysql) ("openssl" ,openssl) - ("pcre" ,pcre) ("python" ,python-2) - ("tinyxml" ,tinyxml) - ("unzip" ,unzip) - ("zip" ,zip) ("freeimage" ,freeimage) ("fftw" ,fftw) ("fftwf" ,fftwf) ("fftw-openmpi" ,fftw-openmpi) - ("atlas" ,atlas) - ("gfortran", gfortran) ("glew" ,glew) ("glu" ,glu) - ("libx11" ,libx11) - ("libxi" ,libxi) - ("libxrandr" ,libxrandr) - ("libxxf86vm" ,libxxf86vm) - ("inputproto" ,inputproto) - ("glproto" ,glproto) ("cmake" ,cmake) ("zlib" ,zlib))) (build-system cmake-build-system) @@ -122,7 +94,7 @@ (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 gpl2+))) + (license gpl3+))) (define-public glfw (package @@ -136,46 +108,30 @@ (sha256 (base32 "1g0jm80cakk60477zz9z1mpsznxaadsfm318yiigf6kackrkqfqg")))) + (build-system cmake-build-system) (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) - (inputs `(("bzip2" ,bzip2) - ("curl" ,curl) + (inputs `(("curl" ,curl) ("dbus" ,dbus) ("enca" ,enca) - ("eudev" ,eudev) - ("fontconfig" ,fontconfig) ("freetype" ,freetype) - ("fribidi" ,fribidi) + ("eudev" ,eudev) ("glew" ,glew) - ("gnutls" ,gnutls) - ("gperf" ,gperf) ("libcap" ,libcap) - ("libgcrypt" ,libgcrypt) ("libjpeg" ,libjpeg) ("libltdl" ,libltdl) - ("libssh" ,libssh) ("libtiff" ,libtiff) - ("libxml2" ,libxml2) - ("libxmu" ,libxmu) - ("libxrandr" ,libxrandr) - ("libxrender" ,libxrender) - ("libxslt" ,libxslt) - ("libxt" ,libxt) - ("lzo" ,lzo) ("mesa-utils" ,mesa-utils) ("mysql" ,mysql) ("openssl" ,openssl) ("python" ,python-2) - ("tinyxml" ,tinyxml) - ("unzip" ,unzip) - ("zip" ,zip) ("zlib" ,zlib))) (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 gpl2))) + (license gpl3+))) -- cgit v1.2.3 From 419f84b3a90ebca9e97537139b89de80ad9e4166 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 01:49:42 +0300 Subject: OpenFYBA package: Cannot build Needs to run autoreconf-ivf before the ./configure phase for the build to be successful. modify-phase statements needed.--- gn/packages/OpenFYBA | 27 ++++++++++----------------- 1 file changed, 10 insertions(+), 17 deletions(-) (limited to 'gn') diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA index 5d64381..fade8de 100644 --- a/gn/packages/OpenFYBA +++ b/gn/packages/OpenFYBA @@ -16,8 +16,8 @@ ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . -(define-module (gnu packages OpenFYBA) - #:use-module ((guix licenses) #:prefix license:) +(define-module (gn packages OpenFYBA) + #:use-module ((guix licenses)) #:use-module (gnu packages) #:use-module (guix packages) #:use-module (guix download) @@ -27,33 +27,26 @@ #: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 "4.4.1") + (version "4.1.1") (source (origin (method url-fetch) - (uri (string-append "https://github.com/kartverket/fyba/archive" + (uri (string-append "https://github.com/kartverket/fyba/archive/" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0ya1agi78d386skq353dk400fl11q6whfqmv31qrkn4g5vamixlr")))) - (inputs `(("openssl" ,openssl) - (build-system gnu-build-system) + (inputs `(("openssl" ,openssl) + ("libgcrypt" ,libgcrypt))) + (build-system gnu-build-system) (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, distributed by the -National Mapping Authority of Norway (Statens kartverk) to read and write -files in the National geodata standard format SOSI. -The original library has a long history, and was originally developed for -systems as diverse as DOS, OS/2-16, OS/2-32, Win16, Win32, and various UNIX -variants (POSIX, HPUX, Silicon graphics). In Norwegian. It shows in the -source code. OpenFYBA has been tested to run at least on Windows and Linux -environments. ") - (license license:gpl2+))) - + (description "OpenFYBA is the source code release of the FYBA library.") + (license gpl2+))) -- cgit v1.2.3 From 2b4c04d952bec10c54ee06bcf6692e0f1da47e0b Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 14:42:35 +0300 Subject: Fixed licensing stuff. Package can now build. Tracking build dependencies.--- gn/packages/arrayfire.scm | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 3244680..060339f 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -69,7 +69,6 @@ ("dbus" ,dbus) ("enca" ,enca) ("eudev" ,eudev) - ("freetype" ,freetype) ("glew" ,glew) ("libcap" ,libcap) ("libjpeg" ,libjpeg) @@ -78,7 +77,6 @@ ("libyajl" ,libyajl) ("mesa-utils" ,mesa-utils) ("mysql" ,mysql) - ("openssl" ,openssl) ("python" ,python-2) ("freeimage" ,freeimage) ("fftw" ,fftw) @@ -86,15 +84,14 @@ ("fftw-openmpi" ,fftw-openmpi) ("glew" ,glew) ("glu" ,glu) - ("cmake" ,cmake) - ("zlib" ,zlib))) + ("cmake" ,cmake))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) (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 gpl3+))) + (license (list gpl2 gpl2+ gpl3 gpl3+)))) (define-public glfw (package @@ -118,7 +115,6 @@ (inputs `(("curl" ,curl) ("dbus" ,dbus) ("enca" ,enca) - ("freetype" ,freetype) ("eudev" ,eudev) ("glew" ,glew) ("libcap" ,libcap) @@ -127,11 +123,9 @@ ("libtiff" ,libtiff) ("mesa-utils" ,mesa-utils) ("mysql" ,mysql) - ("openssl" ,openssl) - ("python" ,python-2) - ("zlib" ,zlib))) + ("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 gpl3+))) + (license (list gpl2)))) -- cgit v1.2.3 From 96ed86cf39e2e973e46edce2c1cb7edce1a2c997 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 17:08:47 +0300 Subject: Show stopper: Cmake variables for glew search paths A bug in Arrayfire. Submitted bug to Arrayfire, waiting for feedback. An interim patch is in the works and is being tested.--- gn/packages/arrayfire.scm | 41 ++++++++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 17 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 060339f..1a1c9a0 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -31,32 +31,31 @@ #:use-module (gnu packages glib) #:use-module (gnu packages image) #:use-module (gnu packages video) - ;;#:use-module (gnu packages tls) #:use-module (gnu packages textutils) #:use-module (gnu packages gl) - ;;#:use-module (gnu packages glew) #:use-module (gnu packages pkg-config) - ;;#:use-module (gnu packages mesa) + #:use-module (gnu packages maths) #:use-module (gnu packages web) #:use-module (gnu packages databases) - ;;#:use-module (gnu packages lapack) #:use-module (gnu packages ldc) - ;;#:use-module (gnu packages gfortran) - #:use-module (gnu packages python) + #:use-module (gnu packages gcc) + #: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 "v3.3.alpha") + (version "3.3.0") (source (origin (method url-fetch) - (uri (string-append "https://github.com/arrayfire/arrayfire/archive/" version - ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "http://arrayfire.com/arrayfire_source/arrayfire-full-" version + ".tar.bz2")) + (file-name (string-append name "-" version ".tar.bz2")) (sha256 (base32 - "0rla0mi5wby8bkpzrj063y6js3d4dlfl3qwfvm8m8skfc21dz52p")))) + "07pbw6vzny3z86y890c0rx7rk31ddchxrrdslk661iq512xppr0g")))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) @@ -70,6 +69,7 @@ ("enca" ,enca) ("eudev" ,eudev) ("glew" ,glew) + ("lapack" ,lapack) ("libcap" ,libcap) ("libjpeg" ,libjpeg) ("libltdl" ,libltdl) @@ -84,10 +84,13 @@ ("fftw-openmpi" ,fftw-openmpi) ("glew" ,glew) ("glu" ,glu) + ("openblas" ,openblas) + ("git" ,git) + ("gcc" ,gcc) ("cmake" ,cmake))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release -DBUILD_OPENCL=ON"))) + `(#: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/") @@ -96,17 +99,16 @@ (define-public glfw (package (name "glfw") - (version "3.0.4") + (version "3.1.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/glfw/glfw/archive/" - version ".zip")) - (file-name (string-append name "-" version ".zip")) + version ".tar.gz")) (sha256 (base32 - "1g0jm80cakk60477zz9z1mpsznxaadsfm318yiigf6kackrkqfqg")))) + "08pixv8hd5xsccf7l8cqcijjqaq4k4da8qbp77wggal2fq445ika")))) (build-system cmake-build-system) - (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) + (arguments `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") #:tests? #f)) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) ("cmake" ,cmake) @@ -122,6 +124,11 @@ ("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/") -- cgit v1.2.3 From 660b3f26943f22a4d816314738ed0b9c8d595299 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 17:25:45 +0300 Subject: Removed obsolete reference to gcc Not needed as an input, deprecated.--- gn/packages/arrayfire.scm | 2 -- 1 file changed, 2 deletions(-) (limited to 'gn') diff --git a/gn/packages/arrayfire.scm b/gn/packages/arrayfire.scm index 1a1c9a0..23ff0af 100644 --- a/gn/packages/arrayfire.scm +++ b/gn/packages/arrayfire.scm @@ -38,7 +38,6 @@ #:use-module (gnu packages web) #:use-module (gnu packages databases) #:use-module (gnu packages ldc) - #:use-module (gnu packages gcc) #:use-module (gnu packages python) #:use-module (gnu packages xorg) #:use-module (gnu packages version-control) @@ -86,7 +85,6 @@ ("glu" ,glu) ("openblas" ,openblas) ("git" ,git) - ("gcc" ,gcc) ("cmake" ,cmake))) (build-system cmake-build-system) (arguments -- cgit v1.2.3 From ddf0498762223a5ac115c635cc9afea1e34b743d Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 21:33:09 +0300 Subject: OpenFYBA ready for production. The package can now be pushed upstream to GNU guix. It builds successfully.--- gn/packages/OpenFYBA | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) (limited to 'gn') diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA index fade8de..cd24003 100644 --- a/gn/packages/OpenFYBA +++ b/gn/packages/OpenFYBA @@ -19,13 +19,14 @@ (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 tls) #:use-module (gnu packages zip) #:use-module (gnu packages gnupg) #:use-module (gnu packages bootstrap) @@ -43,10 +44,18 @@ (sha256 (base32 "0ya1agi78d386skq353dk400fl11q6whfqmv31qrkn4g5vamixlr")))) - (inputs `(("openssl" ,openssl) + (inputs `(("zip" ,zip) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) ("libgcrypt" ,libgcrypt))) - (build-system gnu-build-system) + (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 gpl2+))) + (license (list gpl2)))) -- cgit v1.2.3 From 580b89ae4861ca017c62e2cc44288b16076e4a26 Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 22:05:15 +0300 Subject: Renamed as requested Package name is in lower case.--- gn/packages/OpenFYBA | 61 ------------------------------------------------ gn/packages/openfyba.scm | 61 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+), 61 deletions(-) delete mode 100644 gn/packages/OpenFYBA create mode 100644 gn/packages/openfyba.scm (limited to 'gn') diff --git a/gn/packages/OpenFYBA b/gn/packages/OpenFYBA deleted file mode 100644 index cd24003..0000000 --- a/gn/packages/OpenFYBA +++ /dev/null @@ -1,61 +0,0 @@ -;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Dennis Mungai -;;; -;;; 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 . - -(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)))) diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm new file mode 100644 index 0000000..c345f18 --- /dev/null +++ b/gn/packages/openfyba.scm @@ -0,0 +1,61 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Dennis Mungai +;;; +;;; 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 . + +(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)))) -- cgit v1.2.3 From ac58f720f1de5927973a2167142b01af8b421fbc Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 22:06:33 +0300 Subject: Update openfyba.scm --- gn/packages/openfyba.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/openfyba.scm b/gn/packages/openfyba.scm index c345f18..2b20d09 100644 --- a/gn/packages/openfyba.scm +++ b/gn/packages/openfyba.scm @@ -34,7 +34,7 @@ (define-public openfyba (package - (name "OpenFYBA") + (name "openfyba") (version "4.1.1") (source (origin (method url-fetch) -- cgit v1.2.3 From ef781382de7febeec2b4b8f854c88923d9f72e5f Mon Sep 17 00:00:00 2001 From: Dennis E. Mungai Date: Mon, 29 Feb 2016 22:39:14 +0300 Subject: Added hyphy.scm Requires a patch or substitute* clause to get working.--- gn/packages/hyphy.scm | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 105 insertions(+) create mode 100644 gn/packages/hyphy.scm (limited to 'gn') 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 +;;; +;;; 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 . + +(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+)))) + + + -- cgit v1.2.3 From 010d126f628d10ce82e28a10b58c0db73b61c1da Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 1 Mar 2016 06:16:31 +0000 Subject: hyphy: simplified inputs, changed license --- gn/packages/hyphy.scm | 63 +++++++++++++++++---------------------------------- 1 file changed, 21 insertions(+), 42 deletions(-) (limited to 'gn') diff --git a/gn/packages/hyphy.scm b/gn/packages/hyphy.scm index 23c0406..fea73a4 100644 --- a/gn/packages/hyphy.scm +++ b/gn/packages/hyphy.scm @@ -17,7 +17,7 @@ ;;; along with GNU Guix. If not, see . (define-module (gn packages hyphy) - #:use-module ((guix licenses)) + #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) @@ -54,52 +54,31 @@ (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))) + (inputs + `(("python" ,python-2) + ("fftw-openmpi" ,fftw-openmpi))) (build-system cmake-build-system) (arguments '(#:phases (modify-phases %standard-phases - (add-after 'unpack `bootstrap - (lambda _ - (zero? (system* "make" "MPI"))))))) + (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. ") + `(#: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+)))) + (license license:expat))) -- cgit v1.2.3 From 7d5d0e85fd8c241d186ceb33d200c26319a95ecf Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 1 Mar 2016 09:47:56 +0000 Subject: gn2 updated --- gn/packages/genenetwork.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gn') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 033bf94..e7ebf41 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -141,20 +141,20 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "9e9475053")) + (let ((commit "8c9de7e5a2016f1e5b7397be1a8e84396e3a25c5")) (package (name "genenetwork2") - (version (string-append "2.0-" commit )) + (version (string-append "2.0-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") (url "https://github.com/pjotrp/genenetwork2.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) + "1i8shsqci73z8gsswjack6l1wbph4x3d7vdg4ah8j6r2zsaf5782")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3 From c9c9ff5f70e0fbb08c6b15d9cfc7a541b34cc818 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Tue, 1 Mar 2016 09:53:12 +0000 Subject: gn2 updated --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e7ebf41..aec305b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,7 +154,7 @@ (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 - "1i8shsqci73z8gsswjack6l1wbph4x3d7vdg4ah8j6r2zsaf5782")))) + "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) -- cgit v1.2.3