BWA installation problems

[Amorvincit]

Similar (?) iMAC BWA install difficulties

Snowlion (10.6.8)
Downloaded bwa-0.6.0.tar.bz2 (129.9 kB)

./configure generates the error "No such file or directory"
as does sh: ./autogen.sh (not sure whether there is a Mac equivalent of this GNU Libtool?)

and make throws the following errors:

gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
bntseq.c: In function ‘bwa_fa2pac’:
bntseq.c:275: warning: implicit declaration of function ‘getopt’
bntseq.c:280: error: ‘optind’ undeclared (first use in this function)
bntseq.c:280: error: (Each undeclared identifier is reported only once
bntseq.c:280: error: for each function it appears in.)

and doesn't compile. Can anyone offer any advice?

[xl1]

Segmentation fault - installation problem of BWA?

Hi,

Am I facing the installation problem of bwa-0.5.9rc1, as I am getting the following error:

[bwa_index] Pack FASTA... 68.61 sec
[bwa_index] Reverse the packed sequence... 20.18 sec
[bwa_index] Construct BWT for the packed sequence...
/ebi/lsf/ebi-spool/1311867442.7388100: line 8: 11897 Segmentation fault (core dumped) bwa index /net/isilon7/nobackup/services/embl/dist/xin/cram/Mus_musculus.NCBIM37.63.dna.toplevel.fa > /net/isilon7/nobackup/services/embl/dist/xin/cram/Mus_musculus.NCBIM37.63.dna.toplevel.fa.index

[lh3]

It is possible that bwa does not work on a big-endian CPU (x86 is little-endian while powerpc is big-endian). I have not tried.

[zxl124]

Just type "make" and copy the "bwa" binary anywhere you want.

I have another bwa installation problem. I installed bwa on 3 different Mac.
One is a 64 bit intel dual-core. I did what you said here, it runs just fine.
The second one is a PowerMac G5 dual-core 32bit. There was an error if I just type "make". So I edited two places in Makefile, changing 64 to 32. It worked and bwa runs fine.
The third one is a PowerMac G5 single core 32bit. Again I did the same thing as the other 32 bit Mac. "make" runs through without error message. However, when I tried to run "bwa aln ...". It sends an error message "calculate SA coordinates: Segmentation fault" and quits.

Any idea how to fix this?
Thanks.

[seq_GA]

Thanks Li. It works.

[lh3]

Just type "make" and copy the "bwa" binary anywhere you want.

[sperry]

Try running 'sh ./autogen.sh'. This should create the configure script for you, so long as you have the GNU autotools package installed.

cd bwa-0.5.6
sh ./autogen.sh
./configure
make

This works for me in Ubuntu 9.10 (64bit)

-Scott

[seq_GA]

After downloading bwa-0.5.6.tar.bz2, I used the following command to untar.

tar -xvf bwa-0.5.6.tar.bz2 
cd bwa-0.5.6

The INSTALL documents require us to r un the following three commands to install

./configure; 
make;
 make install'

But there are no ./configure command available. Only configure.in and config.h.in are available. Hence I started with the second command "make".

Can anyone tell me the steps involved in installation? Thanks.