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Old 02-15-2010, 06:37 PM   #1
yasu
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Location: Japan

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Default BWA 'make' error

I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this;

=========
$ make
make[1]: Entering directory `/home/yago/bwa-0.5.6'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6'
make[1]: Entering directory `/home/yago/bwa-0.5.6/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o
utils.c:32:18: error: zlib.h: No such file or directory
In file included from utils.c:33:
utils.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
utils.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
make: *** [utils.o] Error 1
=========

Any suggestions? Thanks a lot!
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Old 02-15-2010, 07:48 PM   #2
drio
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Default

Quote:
Originally Posted by yasu View Post
I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this;

=========
$ make
make[1]: Entering directory `/home/yago/bwa-0.5.6'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6'
make[1]: Entering directory `/home/yago/bwa-0.5.6/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o
utils.c:32:18: error: zlib.h: No such file or directory
In file included from utils.c:33:
utils.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
utils.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
make: *** [utils.o] Error 1
=========

Any suggestions? Thanks a lot!
Install the zlib package (zlib and zlib-devel) in your linux distribution.

debian/ubuntu

$ sudo apt-get install zlib-dev

redhat/fedora

$ sudo yum install zlib-dev
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Old 02-16-2010, 12:25 AM   #3
yasu
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Thanks, drio!!
'$ sudo yum install zlib-devel' DOES work!!
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Old 12-23-2010, 04:55 AM   #4
xujie
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Join Date: Nov 2010
Posts: 11
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Thank you
that works
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