gatk-3.8/public/c/bwa/README.md

BWA C Aligner JNI Library

Basic Instructions

• Download BWA svn revision 47
• Run autoconf and build bwa to create libbwacore.a
• Build mac or linux specific libbwa
• Update the libary path to point to the directory with libbwa

Obtaining compatible libbwacore

libbwa only works with a very specify range of versions from bwa's svn archive. r25-r47 are known to compile a libbwacore.a compatible with building libbwa.so or libbwa.dylib.

From the bwa directory, download bwa revision 47 from svn by running the command:

svn co http://svn.code.sf.net/p/bio-bwa/code/trunk/bwa@47 bwasvn47

Compiling libbwacore.a

Once bwa has been downloaded from svn to the directory bwasvn47, using autoconf and make, one can compile libbwacore.a.

• Install autoconf on Mac using MacPorts port install autoconf

• Or add autoconf on Linux via the dotkit reuse .autoconf-2.69

• Change directory to bwasvn47 cd bwasvn47

• Change permissions to make autogen.sh script executable chmod +x autogen.sh

• Run configure ./configure

• Build make

• Return to the bwa directory cd ..

Compiling libbwa.so / libbwa.dylib

After successfully compiling libbwacore.a from the bwa svn source, the GATK specific libbwa.so / libbwa.dylib may be compiled using libbwacore. There are two shell scripts that include libbwacore.a by using paths pointing to bwasvn47.

• On Mac run ./build_mac.sh
• On Linux run ./build_linux.sh

Running the GATK with libbwa.so / libbwa.dylib

The GATK loads libbwa.so or libbwa.dylib from a directory specified appended to the java.library.path. There are two ways to specify this directory containing libbwa. Either add the directory to the LD_LIBRARY_PATH environment variable export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<lib_dir>, or set java.library.path java variable on the command line -Djava.library.path=<lib_dir>.