metal: Meta-analysis of genomewide association scans

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: metal: Meta-analysis of genomewide association scans
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 30 Aug 2017 18:50:36 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Aug 30 13:50:36 2017 -0500
Changeset:	726b89f6e9d3802151ec4c830f74548677a5227f

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

Log Message:
metal: Meta-analysis of genomewide association scans

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=726b89f6e9d3802151ec4c830f74548677a5227f

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

diffstat:
 Makefile                     |   1 +
 metal/DESCR                  |   9 ++++
 metal/Makefile               |  31 ++++++++++++++
 metal/PLIST                  |   2 +
 metal/distinfo               |   7 +++
 metal/patches/patch-Makefile | 100 +++++++++++++++++++++++++++++++++++++++++++
 6 files changed, 150 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 00c9557cfd..498a1a1585 100644
--- a/Makefile
+++ b/Makefile
@@ -1961,6 +1961,7 @@ SUBDIR+=	memdump
 SUBDIR+=	memgrep
 SUBDIR+=	menumaker
 SUBDIR+=	meta-tracker
+SUBDIR+=	metal
 SUBDIR+=	metalog
 SUBDIR+=	metasploit
 SUBDIR+=	mg-cvs
diff --git a/metal/DESCR b/metal/DESCR
new file mode 100644
index 0000000000..9ccfc789a5
--- /dev/null
+++ b/metal/DESCR
@@ -0,0 +1,9 @@
+METAL is a tool for meta-analysis genomewide association scans. METAL can
+combine either (a) test statistics and standard errors or (b) p-values across
+studies (taking sample size and direction of effect into account). METAL
+analysis is a convenient alternative to a direct analysis of merged data from
+multiple studies. It is especially appropriate when data from the individual
+studies cannot be analyzed together because of differences in ethnicity,
+phenotype distribution, gender or constraints in sharing of individual level
+data imposed. Meta-analysis results in little or no loss of efficiency compared
+to analysis of a combined dataset including data from all individual studies.
diff --git a/metal/Makefile b/metal/Makefile
new file mode 100644
index 0000000000..208b07cf60
--- /dev/null
+++ b/metal/Makefile
@@ -0,0 +1,31 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Aug 30 13:36:06 CDT 2017               #
+###########################################################
+
+## For twister, and double check
+##LICENSE_FILE=	LICENSE.twister
+
+DISTNAME=	generic-metal-2011-03-25
+PKGNAME=	metal-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://csg.sph.umich.edu/abecasis/Metal/download/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://genome.sph.umich.edu/wiki/METAL_Program
+COMMENT=	Meta-analysis of genomewide association scans
+# Check this
+LICENSE=	modified-bsd
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+WRKSRC=		${WRKDIR}/generic-metal
+INSTALL_TARGET=	install-strip
+
+PORTVERSION=	2011.03.25
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/metal/PLIST b/metal/PLIST
new file mode 100644
index 0000000000..031317f9ad
--- /dev/null
+++ b/metal/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/metal
diff --git a/metal/distinfo b/metal/distinfo
new file mode 100644
index 0000000000..702ab45276
--- /dev/null
+++ b/metal/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (generic-metal-2011-03-25.tar.gz) = 5b1e497f6d531145d5207d4fd945ea6bf3402af9
+RMD160 (generic-metal-2011-03-25.tar.gz) = b4b5e57dcd63bb6996e2b2a59f6bad6a74ba0078
+SHA512 (generic-metal-2011-03-25.tar.gz) = 36756c3beecfda5a4bb1333387d6819adb295d2b66677919d59fa037e4b5424e1ff40d165cd4a6cbed31684312ee5e1775795712904727fdd29c5450210ad9a3
+Size (generic-metal-2011-03-25.tar.gz) = 461431 bytes
+SHA1 (patch-Makefile) = 62eb8c43ec3911ddb5d4204c772358d1ab3d7d4b
diff --git a/metal/patches/patch-Makefile b/metal/patches/patch-Makefile
new file mode 100644
index 0000000000..89d132866e
--- /dev/null
+++ b/metal/patches/patch-Makefile
@@ -0,0 +1,100 @@
+$NetBSD$
+
+# Respect environment, use standard make vars, add destdir support
+--- Makefile.orig	2011-03-25 11:16:03.000000000 +0000
++++ Makefile
+@@ -4,17 +4,20 @@
+ #
+ 
+ # version information
+-TOOL = metal
++TOOL =	metal
+ 
+ # default installation directory
+-INSTALLDIR=/usr/local/bin
++PREFIX ?=	/usr/local
++INSTALLDIR =	${PREFIX}/bin
++INSTALL ?=	install
++STRIP ?=	strip
+ 
+ # default C++ compiler
+-CXX=g++ 
++CXX ?=		g++ 
+ 
+ # default compilation flags are 
+ #
+-# CFLAGS=-O2 -I./libsrc/ -I./pdf/
++# CXXFLAGS=-O2 -I./libsrc/ -I./pdf/
+ # 
+ # The following special options may also be added to the default
+ # 
+@@ -27,7 +30,7 @@ CXX=g++ 
+ #                                    on systems where gcc supports the long
+ #                                    long data type and on Windows.
+ # 
+-CFLAGS=-O2 -I./libsrc -I./pdf  -D_FILE_OFFSET_BITS=64 -static
++CXXFLAGS=-O2 -I./libsrc -I./pdf  -D_FILE_OFFSET_BITS=64
+ 
+ # executable file names and locations
+ BINDIR = executables
+@@ -78,7 +81,7 @@ help : 
+ 	@echo "Type...           To..."
+ 	@echo "make help         Display this help screen"
+ 	@echo "make all          Compile everything "
+-	@echo "make install      Install binaries in $(INSTALLDIR)"
++	@echo "make install      Install binaries in $(DESTDIR)$(INSTALLDIR)"
+ 	@echo "make install INSTALLDIR=directory_for_binaries"
+ 	@echo "                  Install binaries in directory_for_binaries"
+ 	@echo "make clean        Delete temporary files"
+@@ -93,7 +96,7 @@ $(BINDIR) :
+ 
+ # dependencies for executables
+ $(TARGET) : $(LIBFILE) $(TOOLSRC) $(PDFLIB)
+-	$(CXX) $(CFLAGS) -o $@ -include version/VersionInfo.h $(TOOL)/*.cpp $(PDFLIB) $(LIBFILE) -lm -lz
++	$(CXX) $(CXXFLAGS) -o $@ -include version/VersionInfo.h $(TOOL)/*.cpp $(PDFLIB) $(LIBFILE) -L$(PREFIX)/lib -lm -lz
+ 
+ $(LIBFILE) : $(LIBOBJ) $(LIBHDR)
+ 	ar -cr $@ $(LIBOBJ)
+@@ -110,20 +113,23 @@ $(PDFOBJ) : $(PDFHDR)
+ clean :
+ 	-rm -f */*.a */*.o $(EXECUTABLES) 
+ 
+-install : all $(INSTALLDIR)
++install : all $(DESTDIR)$(INSTALLDIR)
+ 	@echo " "
+-	@echo Installing to directory $(INSTALLDIR)
++	@echo Installing to directory $(DESTDIR)$(INSTALLDIR)
+ 	@echo To select a different directory, run
+ 	@echo " "
+ 	@echo make install INSTALLDIR=your_preferred_dir
+ 	@echo " "
+-	cp $(EXECUTABLES) $(INSTALLDIR)
++	$(INSTALL) -c $(EXECUTABLES) $(DESTDIR)$(INSTALLDIR)
+ 
+-$(INSTALLDIR) :
++install-strip : install
++	$(STRIP) $(DESTDIR)$(INSTALLDIR)/$(TOOL)
++
++$(DESTDIR)$(INSTALLDIR) :
+ 	@echo " "
+-	@echo Creating directory $(INSTALLDIR)
++	@echo Creating directory $(DESTDIR)$(INSTALLDIR)
+ 	@echo " "
+-	@mkdir -p $(INSTALLDIR)
++	@mkdir -p $(DESTDIR)$(INSTALLDIR)
+ 
+ new-version :
+ 	mkdir -p $(DISTRIBDIR) $(DISTRIBDIR)/$(TOOL)
+@@ -149,10 +155,10 @@ fetch : 
+ 	echo "\n"                         >> version/VersionInfo.h
+ 
+ .c.o :
+-	$(CXX) $(CFLAGS) -o $@ -c $*.c
++	$(CXX) $(CXXFLAGS) -o $@ -c $*.c
+ 
+ .cpp.o : 
+-	$(CXX) $(CFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\"
++	$(CXX) $(CXXFLAGS) -o $@ -c $*.cpp -DVERSION=\"$(VERSION)\"
+ 
+ archive : clean
+ 	mkdir -p generic-$(TOOL)
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