Installing VCFTools on CentOS 7

Question

[sarajeanne08]

Hi All,

I am fairly new to Linux CentoOS 7 and I am trying to install VCFtools. I have git and downloaded the package:

[root@cam-vbl-ds01 ~]# git clone https://github.com/vcftools/vcftools.git

Cloning into 'vcftools'...

remote: Counting objects: 445, done.

remote: Total 445 (delta 0), reused 0 (delta 0), pack-reused 445

Receiving objects: 100% (445/445), 736.51 KiB | 0 bytes/s, done.

Resolving deltas: 100% (190/190), done.

but now I am having issues installing VCFtools. Below is my error message when running the first command according to the getting started page for VCFtools:

[root@cam-vbl-ds01 ~]# cd vcftools/

[root@cam-vbl-ds01 vcftools]# ./autogen.sh

./autogen.sh: line 3: autoreconf: command not found

Can you please help me with this? Thank you in advance.

Sara

[GenoMax]

Can you check if the autoconf package is installed? If not present install it. Some directions here.

[sarajeanne08]

Thank you! I just had a rdp of Linux installed for me - nothing else was setup. I am installing the development tools now. I was able to autoconf and it now looks like I need the zlib package:

configure: error: Package requirements (zlib) were not met:

No package 'zlib' found

Where would I best find that package? Thank you!

[GenoMax]

Find and install zlib-devel package for Cent OS.

[sarajeanne08]

I tried to run the program but it looks like it may not like my vcf file:

--vcf<all_sample.vcf>

bash: syntax error near unexpected token `newline'

I assume this means the format of the file I received is not correct?

[GenoMax]

You should post this as a new question since it is not related to the original one you had posted. Provide the full command line (you can obfuscate file names/paths if you don't want to include real ones).

Answer 1

[sarajeanne08]

Thank you very much for your help. I was able to continue the installation process after installing zlib-devel.