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gatk-3.8/c/bwa/build_linux.sh

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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
2009-11-07 02:41:01 +08:00
#!/bin/sh
Checkpoint. Add first phase of single alignment interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 03:03:43 +08:00
export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa"
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
2009-11-07 02:41:01 +08:00
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