Compiling Burrows-Wheeler Aligner
Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.[1]
Download
Download the latest .tar.gz (aka "tarball") from the SourceForge site for this project: http://sourceforge.net/projects/bio-bwa/files/ Expand the tarball:
[juser@proteusa01 src]$ tar zxf bwa-0.n.m.tar.gz
Alternatively, there seems to be a fork at Github: https://github.com/lh3/bwa
Download the master:
[juser@proteusa01 src]$ git clonehttps://github.com/lh3/bwa
This creates a directory named bwa. Then, follow the instructions below.
Environment
Make sure to load the latest gcc:
[juser@proteusa01 ~]$ module load gcc
Modify Makefile and Compile
Update the optimization flags in the Makefile:
CFLAGS= -Wall -O3 -msse4.2 -mavx -mfpmath=sse
Compile:
[juser@proteusa01 bwa-0.n.m]$ make > Make.out 2>&1 &
Precompiled Version
A locally-compiled version, compiled with the Makefile modification above, can be found in:
/mnt/HA/opt/src/bwa-0.7.7
You may copy that directory structure to your installation location.
Documentation
Documentation is online in the form of a man page. Do:
man bwa
Running BWA
BWA can run with multiple threads. If multi-threaded BWA is needed, request a number of slots equal to the number of threads:
#$ -pe shm 16
...
bwa -t $NSLOTS ...