Installing Vcftools

Question

[nwaforcharles]

Hi, guys please i need some help because i am not confident with linux first i have managed to installed ubuntu on a vitual box on my windows 7 and now i want to install vcf tools and make exeutable files please how can i do this. thanks

Answer 1

[Johan]

This is from the installation instruction in the read me:

Compiling:
To compile and install VCFtools, you should type 'make' in the vcftools folder. The perl scripts and cpp executable will be installed in the /vcftools_(version_num)/bin/ folder. It is recommended that you add this folder to you PATH.

So, go to the folder where you have extracted vcftools by typing:

cd [path-to-vcf-tools]
make

Then you can add it to your path, if you like, (so that you can run the tools by typing there name on the command line, rather then referencing them exactly) by following the instructions here.

Alternative way:
If you have the Ubuntu universe repositories enabled you can install it from there (of course assuming that you are running Ubuntu). Just open a terminal and type:

sudo apt-get install vcftools

Hope you get it working.

Edit 1: Fixed formatting.

Edit 2: Added easier way to install vcftools in from the Ubuntu universe repositories

Answer 2

[nwaforcharles]

ok, thanks a lot

but it is giving me this type of message

i dont know why, or what it means

bilbo@ubuntu:~/tabix-0.2.3$ "make"
make[1]: Entering directory `/home/bilbo/tabix-0.2.3'
gcc -g -Wall -O2 -fPIC  -o tabix main.o -lm  -lz -L. -ltabix
./libtabix.a(bgzf.o): In function `deflate_block':
/home/bilbo/tabix-0.2.3/bgzf.c:300: undefined reference to `deflate'
/home/bilbo/tabix-0.2.3/bgzf.c:302: undefined reference to `deflateEnd'
/home/bilbo/tabix-0.2.3/bgzf.c:294: undefined reference to `deflateInit2_'
/home/bilbo/tabix-0.2.3/bgzf.c:318: undefined reference to `deflateEnd'
/home/bilbo/tabix-0.2.3/bgzf.c:334: undefined reference to `crc32'
/home/bilbo/tabix-0.2.3/bgzf.c:335: undefined reference to `crc32'
./libtabix.a(bgzf.o): In function `inflate_block':
/home/bilbo/tabix-0.2.3/bgzf.c:368: undefined reference to `inflateInit2*'
/home/bilbo/tabix-0.2.3/bgzf.c:373: undefined reference to `inflate'
/home/bilbo/tabix-0.2.3/bgzf.c:379: undefined reference to `inflateEnd'
/home/bilbo/tabix-0.2.3/bgzf.c:375: undefined reference to `inflateEnd'
collect2: ld returned 1 exit status
make[1]: *** [tabix] Error 1
make[1]: Leaving directory</code>/home/bilbo/tabix-0.2.3'
make: *** [all-recur] Error 1
bilbo@ubuntu:~/tabix-0.2.3$

[Johan]

I just noticed that vcf-tools is available in the Ubuntu universe repositories, so there is an easier way to do this. Just enter the terminal and type: sudo apt-get install vcftools It will prompt you for your password, enter it then you should be able to use the program.