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Khalid Shakir 2c854e554a Refactored maven directories and java packages replacing "sting" with "gatk". 
To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
 		2014-05-19 17:36:39 -04:00
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Makefile Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
README.md Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
build_linux.sh Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
build_mac.sh Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
bwa_gateway.cpp At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
bwa_gateway.h At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.cpp Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
org_broadinstitute_gatk_engine_alignment_bwa_c_BWACAligner.h Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00

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>.