diff options
| -rw-r--r-- | 4store-fix-buildsystem.patch | 56 | ||||
| -rw-r--r-- | gn/packages/4store.scm | 86 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 57 | ||||
| -rw-r--r-- | gn/packages/mongodb.scm | 74 | ||||
| -rw-r--r-- | mongodb-add-version-file.patch | 10 |
5 files changed, 283 insertions, 0 deletions
diff --git a/4store-fix-buildsystem.patch b/4store-fix-buildsystem.patch new file mode 100644 index 0000000..a72c4d4 --- /dev/null +++ b/4store-fix-buildsystem.patch @@ -0,0 +1,56 @@ +This patch sets a fixed version to avoid needing Git and the .git/ folder. +It also removes the creation of "/var/lib/4store", which is not available +during the install phase in GNU Guix. + +Patch by Roel Janssen <roel@gnu.org> +*** 4store-1.1.6-orig/configure.ac Wed Feb 4 19:05:24 2015 +--- 4store-1.1.6/configure.ac Wed Mar 23 11:20:38 2016 +*************** +*** 2,13 **** + # Process this file with autoconf to produce a configure script. + + AC_PREREQ([2.50]) +! AC_INIT([4store], m4_esyscmd([./version.sh .version]), [http://4store.org/support/], [4store]) + AC_CONFIG_SRCDIR([src/backend/backend-intl.h]) +! AM_INIT_AUTOMAKE([1.7 std-options -Wall]) + AC_CONFIG_HEADERS(4store-config.h) + + # Checks for programs. + AC_PROG_LIBTOOL + AC_PROG_AWK + AC_PROG_CC +--- 2,14 ---- + # Process this file with autoconf to produce a configure script. + + AC_PREREQ([2.50]) +! AC_INIT([4store], [1.1.6], [http://4store.org/support/], [4store]) + AC_CONFIG_SRCDIR([src/backend/backend-intl.h]) +! AM_INIT_AUTOMAKE([1.7 std-options foreign -Wall]) + AC_CONFIG_HEADERS(4store-config.h) + + # Checks for programs. ++ AM_PROG_AR + AC_PROG_LIBTOOL + AC_PROG_AWK + AC_PROG_CC + +*** 4store-1.1.6-orig/src/utilities/Makefile.am Wed Feb 4 19:05:24 2015 +--- 4store-1.1.6/src/utilities/Makefile.am Wed Mar 23 14:05:56 2016 +*************** +*** 13,20 **** + noinst_PROGRAMS = lex-file-verify 4s-rid + + install-data-local: +! mkdir -p $(DESTDIR)@FS_STORE_ROOT@ +! chmod 1777 $(DESTDIR)@FS_STORE_ROOT@ + + 4s_backend_destroy_SOURCES = backend-destroy.c + 4s_backend_destroy_LDADD = ../common/lib4sintl.a +--- 13,19 ---- + noinst_PROGRAMS = lex-file-verify 4s-rid + + install-data-local: +! echo "Please create the following directory: " $(DESTDIR)@FS_STORE_ROOT@ + + 4s_backend_destroy_SOURCES = backend-destroy.c + 4s_backend_destroy_LDADD = ../common/lib4sintl.a diff --git a/gn/packages/4store.scm b/gn/packages/4store.scm new file mode 100644 index 0000000..41e3249 --- /dev/null +++ b/gn/packages/4store.scm @@ -0,0 +1,86 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Roel Janssen <roel@gnu.org> +;;; +;;; 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 4store) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (gnu packages) + #:use-module (gnu packages autotools) + #:use-module (gnu packages python) + #:use-module (gnu packages perl) + #:use-module (gnu packages rdf) + #:use-module (gnu packages pcre) + #:use-module (gnu packages avahi) + #:use-module (gnu packages gettext) + #:use-module (gnu packages glib) + #:use-module (gnu packages linux) + #:use-module (gnu packages readline) + #:use-module (gnu packages cyrus-sasl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages tls) + #:use-module (gnu packages file) + #:use-module (gnu packages xml)) + +(define-public 4store + (let ((commit "c5a56d7c7504551a1f2fff6c16c4d9a440e4a317")) + (package + (name "4store") + (version (string-append "1.1.6-0." (string-take commit 7))) + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/garlik/4store/archive/" + commit ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "12pn5masjrfp1d8v1dz47qga0ns8d03f2f5icnb9d6m1jfp8l38a")) + (patches (list (search-patch "4store-fix-buildsystem.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("perl" ,perl) + ("python" ,python-2) + ("file" ,file) + ("autoconf" ,autoconf) + ("automake" ,automake) + ("gettext" ,gnu-gettext) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("glib" ,glib) + ("rasqal" ,rasqal) + ("libxml2" ,libxml2) + ("raptor2" ,raptor2) + ("readline" ,readline) + ("avahi" ,avahi) + ("pcre" ,pcre) + ("cyrus-sasl" ,cyrus-sasl) + ("openssl" ,openssl) + ("util-linux" ,util-linux))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'generate-configure + (lambda _ + (zero? (system* "./autogen.sh"))))))) + (home-page "http://www.4store.org") + (synopsis "Clustered RDF storage and query engine") + (description "4store is a RDF/SPARQL store written in C, either single +machines or networked clusters.") + (license license:gpl3+)))) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a4d14b0..1f6052e 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -6,6 +6,7 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) @@ -1287,3 +1288,59 @@ single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.") (license license:gpl3+))) + +(define-public varscan + (package + (name "varscan") + (version "2.4.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/dkoboldt/varscan/releases/download/v" + version "/VarScan.v" version ".source.jar")) + (sha256 + (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8")))) + (build-system ant-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda _ + (mkdir "source") + (chdir "source") + (and + ;; Unpack the Java archive containing the source files. + (zero? (system* "jar" "xf" (assoc-ref %build-inputs "source"))) + ;; Remove existing compiled output. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (unless (string= (string-take-right file 5) ".java") + (zero? (system* "rm" file)))) + (find-files "." #:directories? #f)))))) + (replace 'build + (lambda _ + (let ((classes '())) + (and + ;; Compile the source files. + (with-directory-excursion "net/sf/varscan/" + (for-each (lambda (file) + (when (string= (string-take-right file 5) ".java") + (zero? (system* "javac" file)) + (cons )) + (find-files "." #:directories? #f))) + ;; Construct the new Java archive. + (zero? (system* "jar" "cfm" "varscan-2.4.1.jar" + "META-INF/MANIFEST.MF" + "net/sf/varscan/*.java"))))))) + (replace 'install + (lambda _ + (let ((out (string-append (assoc-ref %outputs "out") + "/share/java/varscan/"))) + (mkdir-p out) + (install-file "varscan-2.4.1.jar" out))))))) + (home-page "http://dkoboldt.github.io/varscan/") + (synopsis "Variant detection in massively parallel sequencing data") + (description "") + ;; Free for non-commercial use by academic, government, and + ;; non-profit/not-for-profit institutions + (license license:non-copyleft))) diff --git a/gn/packages/mongodb.scm b/gn/packages/mongodb.scm new file mode 100644 index 0000000..8f0c68e --- /dev/null +++ b/gn/packages/mongodb.scm @@ -0,0 +1,74 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Roel Janssen <roel@gnu.org> +;;; +;;; 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 bioinformatics) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix build-system gnu) + #:use-module (gnu packages) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python)) + +(define-public mongodb + (package + (name "mongodb") + (version "3.3.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mongodb/mongo/archive/r" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "01v16j8xbry7m7apwlhiqhgx3zyyk2kadyk2sr9m6k20wnh5j24y")) + (patches (list (search-patch "mongodb-add-version-file.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("scons" ,scons) + ("python" ,python-2) + ("perl" ,perl))) + (arguments + `(#:tests? #f ; There is no 'check' target. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase + (add-after 'unpack 'scons-propagate-environment + (lambda _ + ;; Modify the SConstruct file to arrange for + ;; environment variables to be propagated. + (substitute* "SConstruct" + (("^env = Environment\\(") + "env = Environment(ENV=os.environ, ")))) + (replace 'build + (lambda _ + (zero? (system* "scons" "mongod" "mongo" "mongos")))) + (replace 'install + (lambda _ + (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))) + (install-file "mongod" bin) + (install-file "mongos" bin) + (install-file "mongo" bin))))))) + (home-page "https://www.mongodb.org/") + (synopsis "High performance and high availability document database") + (description "Mongo is a high-performance, high availability, +schema-free document-oriented database. A key goal of MongoDB is to bridge +the gap between key/value stores (which are fast and highly scalable) and +traditional RDBMS systems (which are deep in functionality).") + (license (list agpl3 asl2.0)))) diff --git a/mongodb-add-version-file.patch b/mongodb-add-version-file.patch new file mode 100644 index 0000000..ffcb70e --- /dev/null +++ b/mongodb-add-version-file.patch @@ -0,0 +1,10 @@ +This patch is used to replace the need for git. It's a work-around +for a problem described here: https://jira.mongodb.org/browse/SERVER-21317 + +Patch by Roel Janssen <roel@gnu.org> +--- a/version.json 1970-01-01 01:00:00.000000000 +0100 ++++ b/version.json 2016-03-16 15:10:23.933578071 +0100 +@@ -0,0 +1,3 @@ ++{ ++ "version": "3.3.3-guix-" ++} |