linux-ukbgene: Tool for accessing UK Biobank data

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Oct 31 10:03:45 2018 -0500
Changeset:	c4c3956056b91d9c834d2282c5a6de27d9daf905

Modified Files:
	Makefile
Added Files:
	linux-ukbgene/DESCR
	linux-ukbgene/Makefile
	linux-ukbgene/PLIST
	linux-ukbgene/distinfo
	linux-ukbgene/patches/patch-Makefile

Log Message:
linux-ukbgene: Tool for accessing UK Biobank data

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c4c3956056b91d9c834d2282c5a6de27d9daf905

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                             |  1 +
 linux-ukbgene/DESCR                  |  0
 linux-ukbgene/Makefile               | 20 ++++++++++++++++++++
 linux-ukbgene/PLIST                  |  2 ++
 linux-ukbgene/distinfo               |  7 +++++++
 linux-ukbgene/patches/patch-Makefile | 32 ++++++++++++++++++++++++++++++++
 6 files changed, 62 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 5aa9d21856..063a0eadd3 100644
--- a/Makefile
+++ b/Makefile
@@ -1967,6 +1967,7 @@ SUBDIR+=	linux-module-init-tools
 SUBDIR+=	linux-modutils
 SUBDIR+=	linux-modutils-old
 SUBDIR+=	linux-nfs-utils
+SUBDIR+=	linux-ukbgene
 SUBDIR+=	linux-wlan-ng
 SUBDIR+=	linux24-kernel
 SUBDIR+=	linux24-kernel-headers
diff --git a/linux-ukbgene/DESCR b/linux-ukbgene/DESCR
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/linux-ukbgene/Makefile b/linux-ukbgene/Makefile
new file mode 100644
index 0000000000..a27467e700
--- /dev/null
+++ b/linux-ukbgene/Makefile
@@ -0,0 +1,20 @@
+# $NetBSD$
+
+DISTNAME=	ukbgene_linkset
+PKGNAME=	linux-ukbgene
+CATEGORIES=	biology
+MASTER_SITES=	http://biobank.ndph.ox.ac.uk/showcase/util/
+EXTRACT_SUFX=	.tar
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://biobank.ndph.ox.ac.uk/showcase/util/
+COMMENT=	Tool for accessing UK Biobank data
+#LICENSE=	# TODO: (see mk/license.mk)
+
+WRKSRC=		${WRKDIR} # More than one possibility -- please check manually.
+USE_LANGUAGES=	c++
+
+ONLY_FOR_PLATFORM+=	Linux-*-*
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/linux-ukbgene/PLIST b/linux-ukbgene/PLIST
new file mode 100644
index 0000000000..d7002f708d
--- /dev/null
+++ b/linux-ukbgene/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/ukbgene
diff --git a/linux-ukbgene/distinfo b/linux-ukbgene/distinfo
new file mode 100644
index 0000000000..305b2bece1
--- /dev/null
+++ b/linux-ukbgene/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (ukbgene_linkset.tar) = 4fd2ab4ac29a64615ad9e3f50363d79097baf62e
+RMD160 (ukbgene_linkset.tar) = a310928fcbdad9811fbedb20d556f3140cda098d
+SHA512 (ukbgene_linkset.tar) = ef49e29b3265231f16eb8471758158bff25a2f3ddbac0095f86636a19cefa6c3a68daf7b379635a62324c4d028ba3af856e0d79eb6f669ab1a279a6e55a31c2d
+Size (ukbgene_linkset.tar) = 788480 bytes
+SHA1 (patch-Makefile) = 690e389a75df512ee5c698fa3132bb7beaf2c01e
diff --git a/linux-ukbgene/patches/patch-Makefile b/linux-ukbgene/patches/patch-Makefile
new file mode 100644
index 0000000000..f68bab83d1
--- /dev/null
+++ b/linux-ukbgene/patches/patch-Makefile
@@ -0,0 +1,32 @@
+$NetBSD$
+
+# Respect env, add install target
+
+--- Makefile.orig	2018-03-13 15:49:30.000000000 +0000
++++ Makefile
+@@ -1,12 +1,22 @@
+ CCXXFLAGS=-Dint_lnx -O
+-CXX=g++
++CXX?=g++
+ SHELL=/bin/sh
+ LDLIB=-lz
+ LDLIN=-linterp.1
+-CXXFLAGS=$(CCXXFLAGS)
++CXXFLAGS+=$(CCXXFLAGS)
++
++DESTDIR	?= .
++PREFIX	?= /usr/local
++MKDIR	?= mkdir
++
++all:	ukbgene
+ 
+ ukbgene : ukbgene.o
+-	$(CXX) -o ukbgene $< -L. -lugene -lz
++	$(CXX) -o ukbgene ukbgene.o -L. $(LDFLAGS) -lugene -lz
++
++install:
++	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++	install -c ukbgene $(DESTDIR)$(PREFIX)/bin
+ 
+ clean:
+ 	rm *.o