Installing Bwa On 32 Bit Unix Machine

Question

[always_learning]

Hi All,

I was able to install bwa easily on 64 bit but while I was trying to install on 32 bit, its saying an error.

[uvj@localhost bwa-0.7.5a]$ make

gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o

In file included from ksw.c:28:

/usr/lib/gcc/i686-redhat-linux/4.4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"

ksw.c:48: error: expected specifier-qualifier-list before ‘__m128i’

I tried these recommendation at this website:

http://sourceforge.net/mailarchive/forum.php?thread_name=86A911D6-DEE2-49F4-81CA-529FFB53A359%40sanger.ac.uk&forum_name=bio-bwa-help

but still didn't work !!

Any input on this ?

Answer 1

[Pierre Lindenbaum]

Here are the first lines of my Makefile:

bwa-0.7.4$ more Makefile 
    CC=            gcc
    CFLAGS=        -g -Wall -O2 -msse -mmmx -msse2
    AR=            ar
    DFLAGS=        -DHAVE_PTHREAD
    LOBJS=        utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pai
    r.o
    AOBJS=        QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlit
    e.o \
                is.o bwtindex.o bwape.o kopen.o pemerge.o \
                bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
                bwtsw2_chain.o fastmap.o bwtsw2_pair.o
    PROG=        bwa
    INCLUDES=    
    LIBS=        -lm -lz -lpthread
    (...)

[always_learning]

Thanks !! It works !! But can you please explains these changes you made in makefile actually:

1. CFLAGS= -g -Wall -O2 -msse -mmmx -msse2
2. DFLAGS= -DHAVE_PTHREAD

[Pierre Lindenbaum]

1. I think I got that problem http://stackoverflow.com/questions/16410149
2. allow multithreading

[always_learning]

Thanks !! Some of feature of SSE is not available for 32 bits and SSE is basically supporting 64 bits by design only.