vcftools install on 14.04.3

[cmccabe]

I am installing vcftools from github and have two questions:

1. where do I put the samtools1.2 folder so that the tabix and bgzip index can be used.

I added it to path but am not sure where i should put the download.

2. I am following the install guide as posted on github and not able to do the ./configure or make.

 bash: ./configure: No such file or directory

 make: *** No targets specified and no makefile found.  Stop.

Thank you .

EDIT:

I was able to do the ./configure and make but get an error doing the make install

Making install in src
make[1]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src'
Making install in cpp
make[2]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[3]: Entering directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  [B]/usr/bin/install -c vcftools '/usr/local/bin'
/usr/bin/install: cannot create regular file ‘/usr/local/bin/vcftools’: Permission denied[/B]
make[3]: *** [install-binPROGRAMS] Error 1
make[3]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src/cpp'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/cmccabe/Desktop/ngs_analysis/vcftools-0.1.14/src'
make: *** [install-recursive] Error 1

[GenoMax]

Did you try?

$ sudo make install

[cmccabe]

Yes I did and that worked. I have downloaded tabix and added that to path and will add the Perl5 next, then I should be done. There was no bin folder created as the manual said but we will see. Thanks .

[GenoMax]

If there was no /usr/local/bin on your computer then you can make that folder yourself (with sudo). It is a good idea to install or softlink non-system packages that you install into this folder as a common entity present in your $PATH.

[cmccabe]

There is a /usr/local/bin does that not need to be added to path? I have added the tabix to path:

 echo 'export PATH=$PATH:/home/cmccabe/tabix-0.2.6' >> ~/.bashrc

and now am at the step where I add PERL5 to path

 export PERL5LIB=/home/cmccabe/Desktop/ngs_analysis/vcftools-0.14/src/perl

or

 export PERL5LIB=/home/cmccabe/tabix-0.2.6/perl

Not sure which to use?

Will vcftools be usable then? Thank you .

[GenoMax]

You don't have system Perl? http://askubuntu.com/questions/53068...r-ubuntu-14-04

[cmccabe]

No I do not, I will load that but is that whats needed for the PERL5? I am learning ubuntu and how to best utilize it. Thank you .