Question: vcftools installation: vcftools/bin folder not created
0
gravatar for spider_monkey
3.7 years ago by
spider_monkey10 wrote:

I am attempting to install vcftools on my macOS Sierra (version 10.12.3). I am using the installation instructions from github as follows (from https://github.com/vcftools/vcftools):

git clone https://github.com/vcftools/vcftools.git
cd vcftools
./autogen.sh
./configure
make
sudo make install (I added sudo because otherwise I got permission denied).

Before beginning vcftools installation, I used homebrew to install the following packages: autoconf, pkg-config, automake, libtool, and zlib. zlib is keg-only so I also used homebrew to link it ('brew link --force zlib'). That way, I would not get errors when running ./autogen.sh.

Now, no errors are listed when I run every line. However, a bin folder containing the vcftools executable is never created in my vcftools folder after finishing the installation instructions. What am I doing wrong?

After running 'sudo make install' the following lines are the last ones printed. Does this have anything to do with the fact that a bin folder is not created?
make[3]: Nothing to be done for install-exec-am'. make[3]: Nothing to be done forinstall-data-am'.
make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done forinstall-data-am'.

I would appreciate any feedback. Thank you!

ADD COMMENTlink modified 3.7 years ago by Pierre Lindenbaum131k • written 3.7 years ago by spider_monkey10
1

If you already have Homebrew, it might be easier to just use Homebrew Science.

brew tap homebrew/science
brew install vcftools

See: https://github.com/Homebrew/homebrew-science

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by igor11k
2
gravatar for Pierre Lindenbaum
3.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

However, a bin folder containing the vcftools executable is never created

sudo make install would install it in /usr/local/bin or /usr/bin

try

which vcftools

if you want to install it in a specific directory, you would use

./configure --prefix /path/to/your/dir
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Pierre Lindenbaum131k

Thank you, I understand now! I chose to install it in my vcftools directory and I also entered 'make install' instead of 'sudo make install' like I originally did. Now there is a bin folder containing executables within my vcftools directory. Thanks again!

ADD REPLYlink written 3.7 years ago by spider_monkey10

if it answers , mark my answer as answered (green tick on the left)

ADD REPLYlink written 3.7 years ago by Pierre Lindenbaum131k
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