BWA and Samtools installation failing

[JamesT]

Hi.

First post, so please be gentle

First, I would like to say that I am not very familiar with Linux/Unix so I need advice to be addressed in a manner so that I can understand. I hope this is not stopping you from giving me some advice.

System, Ubuntu 12.04 LTS 64-bit, Intel core i7-2640M CPU, 8 GB memory.

I would like to set up a few tools in order to perform ananlysis of my RNA-sequencing (Illumina HiSeq). So far I have figured out that I would like to try the combination of the following software:

- BWA
- Cufflinks
- Samtools
- Bowtie
- TopHat

Cufflinks and tophat is working (at least if I type cufflinks --help or tophat --help).

Now, I am having trouble with Samtools and BWA, and it appears that I am not able to install them (by using the make command).

I am getting the following error:

JamesT-XPS-L412Z:~/Samtools/samtools-0.1.18$ make
make[1]: Entering directory `/home/jim/Samtools/samtools-0.1.18'
make[2]: Entering directory `/home/jim/Samtools/samtools-0.1.18'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
In file included from bgzf.c:36:0:
bgzf.h:29:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/jim/Samtools/samtools-0.1.18'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/jim/Samtools/samtools-0.1.18'
make: *** [all-recur] Error 1

JamesT-XPS-L412Z:~/bwa/bwa-0.6.2$ make
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o
In file included from bwa.c:8:0:
bntseq.h:32:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [bwa.o] Error 1

From searching the web for a few days I think the problem is with the library, however, my Ubuntu tells me that the zlib1g-dev is installed. Is there any other library I need? Do I need to make changes to the make file? Or is the problem elsewhere.

-James

[JamesT]

I did the following:

JamesT-XPS-L412Z:~$sudo apt-get update
JamesT-XPS-L412Z:~$sudo apt-get install zlib1g-dev libncurses5-dev
JamesT-XPS-L412Z:~/Samtools/samtools-0.1.18$ make
JamesT-XPS-L412Z:~/bwa/bwa-0.6.2$ make

Both commands finished without errors, so I assume things are ok.

[arkal]

Hi.

First, I would like to say that I am not very familiar with Linux/Unix so I need advice to be addressed in a manner so that I can understand. I hope this is not stopping you from giving me some advice.

Don't worry... I'm sure most of us without a backgroud in linux have been stumped by the zlib/ncurses thing at some point or the other

[JamesT]

Well, at least I managed to make it work Thanks for the positive remark, it is helpful when you are entering a new field (NGS and Linux).