install VCFtools on Ubuntu 18

Question: install VCFtools on Ubuntu 18

9 months ago by

Germany, Mannheim, UMM

marongiu.luigi • 380 wrote:

Dear all,

I am trying to install VCFtools on Ubuntu 18. I downloaded VCFtools from the github then added

export PERL5LIB=/path/to/your/vcftools-directory/src/perl/

to bashrc then ran the suggested commands:

cd vcftools/ 
./autogen.sh 
./configure 
make 
make install

but I got:

$ make install
Making install in src
make[1]: Entering directory '/home/gigiux/src/vcftools/src'
Making install in cpp
make[2]: Entering directory '/home/gigiux/src/vcftools/src/cpp'
make[3]: Entering directory '/home/gigiux/src/vcftools/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c vcftools '/usr/local/bin'
/usr/bin/install: cannot create regular file '/usr/local/bin/vcftools': Permission denied
Makefile:402: recipe for target 'install-binPROGRAMS' failed
make[3]: *** [install-binPROGRAMS] Error 1
make[3]: Leaving directory '/home/gigiux/src/vcftools/src/cpp'
Makefile:966: recipe for target 'install-am' failed
make[2]: *** [install-am] Error 2
make[2]: Leaving directory '/home/gigiux/src/vcftools/src/cpp'
Makefile:320: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory '/home/gigiux/src/vcftools/src'
Makefile:363: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

What did go wrong? How can I solve it?

Thank you

vcftools ubuntu • 673 views

ADD COMMENT • link •

modified 9 months ago by dovi • 60 • written 9 months ago by marongiu.luigi • 380

You should also be switching to bcftools since that seems to be the preferred method for those who do this analysis regularly.

ADD REPLY • link written 9 months ago by genomax ♦ 65k

Indeed, even the new VCFtools homepage now has a 'BCFtools touch': https://vcftools.github.io/htslib.html

One should no longer be using VCFtools.

ADD REPLY • link modified 9 months ago • written 9 months ago by Kevin Blighe ♦ 41k

relevant error message: /usr/bin/install: cannot create regular file '/usr/local/bin/vcftools': Permission denied

My suggestion is to move to user land installation tools such as pip, brew/homebrew, conda/bioconda. Usually, they have most recent versions and do not require system wide permissions.

ADD REPLY • link modified 9 months ago • written 9 months ago by cpad0112 ♦ 11k

I was told NOT to use sudo when making thing, anyway it worked:

$ sudo make install
Making install in src
make[1]: Entering directory '/home/gigiux/src/vcftools/src'
Making install in cpp
make[2]: Entering directory '/home/gigiux/src/vcftools/src/cpp'
make[3]: Entering directory '/home/gigiux/src/vcftools/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c vcftools '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/man/man1'
 /usr/bin/install -c -m 644 vcftools.1 '/usr/local/share/man/man1'
make[3]: Leaving directory '/home/gigiux/src/vcftools/src/cpp'
make[2]: Leaving directory '/home/gigiux/src/vcftools/src/cpp'
Making install in perl
make[2]: Entering directory '/home/gigiux/src/vcftools/src/perl'
make[3]: Entering directory '/home/gigiux/src/vcftools/src/perl'
 /bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/perl/5.26.1'
 /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/usr/local/share/perl/5.26.1'
make[3]: Leaving directory '/home/gigiux/src/vcftools/src/perl'
make[2]: Leaving directory '/home/gigiux/src/vcftools/src/perl'
make[2]: Entering directory '/home/gigiux/src/vcftools/src'
make[3]: Entering directory '/home/gigiux/src/vcftools/src'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/gigiux/src/vcftools/src'
make[2]: Leaving directory '/home/gigiux/src/vcftools/src'
make[1]: Leaving directory '/home/gigiux/src/vcftools/src'
make[1]: Entering directory '/home/gigiux/src/vcftools'
make[2]: Entering directory '/home/gigiux/src/vcftools'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/gigiux/src/vcftools'
make[1]: Leaving directory '/home/gigiux/src/vcftools'

the installation seems successful:

$ vcftools

VCFtools (0.1.15)
© Adam Auton and Anthony Marcketta 2009

Process Variant Call Format files

For a list of options, please go to:
    https://vcftools.github.io/man_latest.html

Alternatively, a man page is available, type:
    man vcftools

Questions, comments, and suggestions should be emailed to:
    vcftools-help@lists.sourceforge.net

thank you

ADD REPLY • link written 9 months ago by marongiu.luigi • 380

If using sudo is what fixed the issue then you should accept the answer provided by @dovi below to provide closure to this thread.

You could have also used the method suggested by dovi that places the install somewhere else thus not requiring sudo.

ADD REPLY • link modified 9 months ago • written 9 months ago by genomax ♦ 65k

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