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-rw-r--r--4store-fix-buildsystem.patch56
-rw-r--r--gn/packages/4store.scm86
-rw-r--r--gn/packages/bioinformatics.scm57
-rw-r--r--gn/packages/mongodb.scm74
-rw-r--r--mongodb-add-version-file.patch10
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 3a82c18..68095e9 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)
@@ -1237,3 +1238,59 @@ 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-"
++}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 13:09:43 +0000