bolt-llm: Test association between phenotype and genotypes

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bolt-llm: Test association between phenotype and genotypes
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 20 Sep 2017 11:02:59 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Sep 20 06:02:59 2017 -0500
Changeset:	d1fcda1329d8cf8766de0626ce1b0881e6ca073e

Added Files:
	bolt-llm/DESCR
	bolt-llm/Makefile
	bolt-llm/PLIST
	bolt-llm/distinfo
	bolt-llm/patches/patch-FileUtils.cpp
	bolt-llm/patches/patch-Makefile
	bolt-llm/patches/patch-StringUtils.cpp

Log Message:
bolt-llm: Test association between phenotype and genotypes

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d1fcda1329d8cf8766de0626ce1b0881e6ca073e

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

diffstat:
 bolt-llm/DESCR                         |   4 ++
 bolt-llm/Makefile                      |  38 +++++++++++
 bolt-llm/PLIST                         |   2 +
 bolt-llm/distinfo                      |   9 +++
 bolt-llm/patches/patch-FileUtils.cpp   |  14 ++++
 bolt-llm/patches/patch-Makefile        | 118 +++++++++++++++++++++++++++++++++
 bolt-llm/patches/patch-StringUtils.cpp |  13 ++++
 7 files changed, 198 insertions(+)

diffs:
diff --git a/bolt-llm/DESCR b/bolt-llm/DESCR
new file mode 100644
index 0000000000..2d46a0524c
--- /dev/null
+++ b/bolt-llm/DESCR
@@ -0,0 +1,4 @@
+The BOLT-LMM algorithm computes statistics for testing association between
+phenotype and genotypes using a linear mixed model (LMM)  [1]. By default,
+BOLT-LMM assumes a Bayesian mixture-of-normals prior for the random effect
+attributed to SNPs other than the one being tested.
diff --git a/bolt-llm/Makefile b/bolt-llm/Makefile
new file mode 100644
index 0000000000..695474f1f3
--- /dev/null
+++ b/bolt-llm/Makefile
@@ -0,0 +1,38 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Sep 20 05:34:25 CDT 2017               #
+###########################################################
+
+DISTNAME=	BOLT-LMM_v${PORTVERSION}
+PKGNAME=	bolt-llm-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://data.broadinstitute.org/alkesgroup/BOLT-LMM/
+COMMENT=	Statistics for testing association between phenotype and genotypes
+
+# Check this
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++ fortran
+USE_TOOLS+=	gmake
+
+WRKSRC=		${WRKDIR}/${DISTNAME}/src
+
+CXXFLAGS=	-fopenmp
+BUILD_TARGET=	 bolt
+
+PORTVERSION=	2.3
+
+INSTALLATION_DIRS=	bin
+
+# FIXME: Use openblas when available for better performance
+.include "../../math/nlopt/buildlink3.mk"
+.include "../../math/blas/buildlink3.mk"
+.include "../../math/lapack/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bolt-llm/PLIST b/bolt-llm/PLIST
new file mode 100644
index 0000000000..773027c62d
--- /dev/null
+++ b/bolt-llm/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/bolt
diff --git a/bolt-llm/distinfo b/bolt-llm/distinfo
new file mode 100644
index 0000000000..07becca762
--- /dev/null
+++ b/bolt-llm/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+SHA1 (BOLT-LMM_v2.3.tar.gz) = 4f2caf427cbcbe58175e6e5c711c3d8b0c66a9d6
+RMD160 (BOLT-LMM_v2.3.tar.gz) = d0d207f2993d00607f256edb0e9cda57aa0bd800
+SHA512 (BOLT-LMM_v2.3.tar.gz) = a396bb6699fbb87327901a8db46faa45705405160f318796f887b8cd6edd495f10fa460201a4eead57b2bc34adb45f44d26dd59ae12ed2240d4d46b6b6e959e6
+Size (BOLT-LMM_v2.3.tar.gz) = 336986328 bytes
+SHA1 (patch-FileUtils.cpp) = 258138822f610ab38f9cf3cf0ad03ca49b67ad1c
+SHA1 (patch-Makefile) = f960889320bdcd8e158cd509ae87b65672169ed5
+SHA1 (patch-StringUtils.cpp) = f0a5c3375a95391235d85fc9431524236e39910f
diff --git a/bolt-llm/patches/patch-FileUtils.cpp b/bolt-llm/patches/patch-FileUtils.cpp
new file mode 100644
index 0000000000..7806a59216
--- /dev/null
+++ b/bolt-llm/patches/patch-FileUtils.cpp
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Unused variable
+--- FileUtils.cpp.orig	2017-09-20 10:29:18 UTC
++++ FileUtils.cpp
+@@ -275,7 +275,7 @@ namespace FileUtils {
+     uint Layout = (flags>>2)&0xf; cout << "Layout: " << Layout << endl;
+     assert(Layout==1 || Layout==2); // REQUIRE Layout==1 or Layout==2
+ 
+-    uint SampleIdentifiers = flags>>31; //cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
++    // uint SampleIdentifiers = flags>>31; cout << "SampleIdentifiers: " << SampleIdentifiers << endl;
+     fseek(fin, offset+4, SEEK_SET);
+ 
+     // check first SNP
diff --git a/bolt-llm/patches/patch-Makefile b/bolt-llm/patches/patch-Makefile
new file mode 100644
index 0000000000..01182cc1f5
--- /dev/null
+++ b/bolt-llm/patches/patch-Makefile
@@ -0,0 +1,118 @@
+$NetBSD$
+
+# Respect env
+--- Makefile.orig	2017-08-03 00:14:08.000000000 +0000
++++ Makefile
+@@ -1,28 +1,33 @@
+ ### modify these paths to local Boost and NLopt install directories
+-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
+-NLOPT_INSTALL_DIR = /groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
++BOOST_INSTALL_DIR ?= ${LOCALBASE}
++# NLOPT_INSTALL_DIR ?= ${LOCALBASE}
++
++MKDIR ?=	mkdir
++DESTDIR ?=	.
++PREFIX ?=	/usr/local
++INSTALL ?=	install
+ 
+ MKLROOT = /groups/price/poru/external_software/intel/mkl
+ INTELROOT = /groups/price/poru/external_software/intel
+-ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
+-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
++ZLIB_STATIC_DIR ?= /usr/lib
++GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
+ 
+ ifeq ($(strip ${linking}),)
+ 	linking = dynamic
+ endif
+ 
+-# CC = g++
+-CC = /groups/price/poru/external_software/intel/bin/icpc
++# CXX = g++
++CXX ?= /groups/price/poru/external_software/intel/bin/icpc
+ 
+ ifeq (${debug},true)
+-	CFLAGS += -g
++	CXXFLAGS += -g
+ else
+-	CFLAGS += -O2
++	CXXFLAGS += -O2
+ endif
+ 
+-CFLAGS += -msse -msse2
+-CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
+-CFLAGS += -Wall
++CXXFLAGS += -msse -msse2
++CXXFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
++CXXFLAGS += -Wall
+ 
+ 
+ # add Boost include and lib paths
+@@ -51,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
+ endif
+ 
+ # add MKL paths (if not compiling with g++, i.e., compiling with icpc)
+-ifneq (${CC},g++)
++ifneq (${CXX},${CXX})
+ 	CPATHS += -I${MKLROOT}/include
+ 	ifeq (${linking},dynamic)
+ 		LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
+@@ -60,28 +65,28 @@ ifneq (${CC},g++)
+ endif
+ 
+ # add flags for static linking; build LAPACK/MKL component of link line
+-ifeq (${CC},g++)
+-	CFLAGS += -fopenmp
+-	LFLAGS += -fopenmp
+-	LLAPACK = -llapack -lgfortran
++ifeq (${CXX},${CXX})
++	CXXFLAGS += -fopenmp
++	LDFLAGS += -fopenmp
++	LLAPACK = -llapack -lblas -lgfortran
+ 	ifeq (${linking},static)
+-		LFLAGS += -static
++		LDFLAGS += -static
+ 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
+ 	else ifeq (${linking},static-except-glibc)
+-		LFLAGS += -static-libgcc -static-libstdc++
++		LDFLAGS += -static-libgcc -static-libstdc++
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 	endif
+ else
+-	CFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
+-	CFLAGS += -qopenmp
+-	LFLAGS += -qopenmp
+-	CFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
++	CXXFLAGS += -DUSE_MKL #-DUSE_MKL_MALLOC
++	CXXFLAGS += -qopenmp
++	LDFLAGS += -qopenmp
++	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
+ 	ifeq (${linking},static)
+-		LFLAGS += -static
++		LDFLAGS += -static
+ 		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
+ 	else ifeq (${linking},static-except-glibc)
+-		LFLAGS += -static-intel -static-libstdc++ -static-libgcc
++		LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
+ 	else
+@@ -110,11 +115,15 @@ OMAIN = BoltMain.o $O
+ .PHONY: clean
+ 
+ %.o: %.cpp
+-	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<
++	${CXX} ${CXXFLAGS} ${CPATHS} -o $@ -c $<
+ 
+ $T: ${OMAIN}
+-	${CC} ${LFLAGS} -o $T ${OMAIN} $L
++	${CXX} ${LDFLAGS} -o $T ${OMAIN} $L
+ 
+ clean:
+ 	rm -f *.o
+ 	rm -f $T
++
++install:
++	${MKDIR} ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c -s $T ${DESTDIR}${PREFIX}/bin
diff --git a/bolt-llm/patches/patch-StringUtils.cpp b/bolt-llm/patches/patch-StringUtils.cpp
new file mode 100644
index 0000000000..9aa25f0c38
--- /dev/null
+++ b/bolt-llm/patches/patch-StringUtils.cpp
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Missing header
+--- StringUtils.cpp.orig	2017-08-02 23:43:24 UTC
++++ StringUtils.cpp
+@@ -22,6 +22,7 @@
+ #include <cstdio>
+ #include <iostream>
+ #include <sstream>
++#include <sys/types.h>	// uint
+ 
+ #include "StringUtils.hpp"
+
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