Entering edit mode
6.5 years ago
marongiu.luigi
▴
730
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
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
.