[nilshomer]

I tried to follow the link but it didn't work, so I decided to post my problem.
Thanks to one of my colleagues I find out what was the problem...the ubuntu release in the server wasn't updated...so now everything is working.

Thanks

Laura

Just tried the link, it links to seqanswers.com, so... I am glad you solved the problem.

[Fahim123]

Hi,

I am new in the bio.
I need to install the BWA on my window but have problem by zlib
I have already downloaded the last version of BWA and the zlib and I use the Visual Studio 2017 for compiling.
I do not know how to run.
F:\BIO\bwa>make all
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
utils.c:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [utils.o] Error 1


Would you please help me?

[Sidrah]

Hi,

I am new in the bio.
I need to install the BWA on my window but have problem by zlib
I have already downloaded the last version of BWA and the zlib and I use the Visual Studio 2017 for compiling.
I do not know how to run.
F:\BIO\bwa>make all
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
utils.c:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [utils.o] Error 1


Would you please help me?

Did you find the solution to this problem for windows?? I m also having the same problem.

[musohail]

Hello Colleagues

I have installed BWA-0.7.17 many times. It works fine. It has all the commands in it. It does well with BWA index.
But it doesnt work for bwa mem. saying mem is not a command.
Whe I type only bwa. it gives all other command options except mem.
On my other computer it also have mem command but I do not use that computer. Please help

Usage: bwa <command> [options]

Command: index index sequences in the FASTA format
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
fastmap identify super-maximal exact matches

fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
pac2cspac convert PAC to color-space PAC
stdsw standard SW/NW alignment