Question: install VCFtools on Ubuntu 18
0
gravatar for marongiu.luigi
9 months ago by
Germany, Mannheim, UMM
marongiu.luigi380 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 COMMENTlink modified 9 months ago by dovi60 • written 9 months ago by marongiu.luigi380
2

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

ADD REPLYlink written 9 months ago by genomax65k

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 REPLYlink modified 9 months ago • written 9 months ago by Kevin Blighe41k
2

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 REPLYlink modified 9 months ago • written 9 months ago by cpad011211k

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 REPLYlink written 9 months ago by marongiu.luigi380

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 REPLYlink modified 9 months ago • written 9 months ago by genomax65k
2
gravatar for dovi
9 months ago by
dovi60
dovi60 wrote:

You don't have permissions to write in /usr/local/bin /usr/bin/install: cannot create regular file '/usr/local/bin/vcftools': Permission denied

If you have admin permissions just use sudo make install

If you don't have permissions, try to install vcftools into a folder where you can write by using ./configure --prefix=path/to/folder/with/permission and then continue with make and make install..

ADD COMMENTlink modified 9 months ago • written 9 months ago by dovi60
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