From f73dd0939910ba5ec1112d66323e231ef156643a Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 6 Nov 2009 18:41:01 +0000
Subject: [PATCH] More preparation for bwa patch: create a crude, minimal build
 system to build against a static library that the bwa compile (now)
 generates.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1980 348d0f76-0448-11de-a6fe-93d51630548a
---
 c/bwa/Makefile       | 19 +++++++++++++++++++
 c/bwa/build_linux.sh |  7 +++++++
 c/bwa/build_mac.sh   |  7 +++++++
 c/bwa/bwa_as_lib.sh  | 18 ------------------
 4 files changed, 33 insertions(+), 18 deletions(-)
 create mode 100644 c/bwa/Makefile
 create mode 100755 c/bwa/build_linux.sh
 create mode 100644 c/bwa/build_mac.sh
 delete mode 100644 c/bwa/bwa_as_lib.sh

diff --git a/c/bwa/Makefile b/c/bwa/Makefile
new file mode 100644
index 000000000..5b888fac8
--- /dev/null
+++ b/c/bwa/Makefile
@@ -0,0 +1,19 @@
+CXX=g++
+CXXFLAGS=-g -Wall -O2 -m64 -fPIC
+
+.cpp.o:
+	$(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) $< -o $@
+
+all: init org_broadinstitute_sting_alignment_bwa_BWACAligner.o bwa_gateway.o 
+	$(LIBTOOL_COMMAND) org_broadinstitute_sting_alignment_bwa_BWACAligner.o bwa_gateway.o -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore $(EXTRA_LIBS)
+
+init:
+	@echo Please make sure the following platforms are set correctly on your machine.
+	@echo BWA_HOME=$(BWA_HOME)
+	@echo JAVA_INCLUDE=$(JAVA_INCLUDE)
+	@echo TARGET_LIB=$(TARGET_LIB)
+	@echo EXTRA_LIBS=$(EXTRA_LIBS)
+	@echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND)x
+
+clean:
+	rm *.o libbwa.*
diff --git a/c/bwa/build_linux.sh b/c/bwa/build_linux.sh
new file mode 100755
index 000000000..449b7211e
--- /dev/null
+++ b/c/bwa/build_linux.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+export BWA_HOME="/humgen/gsa-hphome1/hanna/src/bwa-0.5.3"
+export JAVA_INCLUDE="/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include -I/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include/linux"
+export TARGET_LIB="libbwa.so"
+export EXTRA_LIBS="-lc -lz -lstdc++ -lpthread"
+export LIBTOOL_COMMAND="g++ -shared -Wl,-soname,libbwa.so"
+make 
diff --git a/c/bwa/build_mac.sh b/c/bwa/build_mac.sh
new file mode 100644
index 000000000..4a0527288
--- /dev/null
+++ b/c/bwa/build_mac.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+export BWA_HOME="/Users/mhanna/src/bwa-0.5.3"
+export JAVA_INCLUDE="/System/Library/Frameworks/JavaVM.framework/Headers"
+export TARGET_LIB="libbwa.dylib"
+export EXTRA_LIBS="-lc -lz -lsupc++"
+export LIBTOOL_COMMAND="libtool -dynamic"
+make 
diff --git a/c/bwa/bwa_as_lib.sh b/c/bwa/bwa_as_lib.sh
deleted file mode 100644
index 48e22c553..000000000
--- a/c/bwa/bwa_as_lib.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-CFLAGS="-g -Wall -O2 -m64"
-BWA_INCLUDE="/Users/mhanna/src/bwa-0.5.3"
-BWA_SRC="/Users/mhanna/src/bwa-0.5.3"
-
-g++ $CFLAGS -c -I$BWA_INCLUDE -I/System/Library/Frameworks/JavaVM.framework/Headers org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
-g++ $CFLAGS -c -I$BWA_INCLUDE bwa_gateway.cpp -o bwa_gateway.o
-gcc $CFLAGS -c  $BWA_SRC/bntseq.c -o bntseq.o
-gcc $CFLAGS -c $BWA_SRC/bwase.c -o bwase.o
-gcc $CFLAGS -c $BWA_SRC/bwt.c -o bwt.o
-gcc $CFLAGS -c $BWA_SRC/bwtaln.c -o bwtaln.o
-gcc $CFLAGS -c $BWA_SRC/bwtgap.c -o bwtgap.o
-gcc $CFLAGS -c $BWA_SRC/bwtio.c -o bwtio.o
-gcc $CFLAGS -c $BWA_SRC/bwaseqio.c -o bwaseqio.o
-gcc $CFLAGS -c $BWA_SRC/cs2nt.c -o cs2nt.o
-gcc $CFLAGS -c $BWA_SRC/kstring.c -o kstring.o
-gcc $CFLAGS -c $BWA_SRC/stdaln.c -o stdaln.o
-gcc $CFLAGS -c $BWA_SRC/utils.c -o utils.o
-g++ -dynamiclib -o libbwa.dylib org_broadinstitute_sting_alignment_bwa_BWACAligner.o bwa_gateway.o bntseq.o bwase.o bwt.o bwtaln.o bwtgap.o bwtio.o bwaseqio.o cs2nt.o kstring.o stdaln.o utils.o -framework JavaVM -lz
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