Question: install VCFtools on Ubuntu 18
0
marongiu.luigi • 520 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
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modified 2.5 years ago
by
dovi • 60
•
written
2.5 years ago by
marongiu.luigi • 520
You should also be switching to
bcftools
since that seems to be the preferred method for those who do this analysis regularly.Indeed, even the new VCFtools homepage now has a 'BCFtools touch': https://vcftools.github.io/htslib.html
One should no longer be using VCFtools.
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.
I was told NOT to use sudo when making thing, anyway it worked:
the installation seems successful:
thank you
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
.