Question: Basic question about using ./configure for installing a software
gravatar for c_u
14 months ago by
United States
c_u230 wrote:


This is a naive question. I am trying to install Jellyfish ( on a Mac. For that, their docs say ( -

To install in your home directory, do:

./configure --prefix=$HOME 
make -j 4 
make install

Now, I downloaded the git directory on the system, cd'd to it and ran ./configure --prefix=$HOME, and on the terminal, I got the error -

-bash: ./configure: No such file or directory

I had previously installed gcc on the system using brew install gcc. I also tried gcc ./configure --prefix=$HOME, but again the error was -

clang: error: no such file or directory: './configure'

clang: error: no input files

The folder I downloaded from their Github page does have a file names Could someone let me know what is the mistake I am committing? Thanks!!

jellyfish installation • 392 views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 14 months ago by c_u230
gravatar for h.mon
14 months ago by
h.mon29k wrote:

It is all there at the GitHub repository, you didn't read carefully:

To compile from the git tree, you will also need autoconf, automake, libool, gettext, pkg-config and yaggo. Then to compile and install (in /usr/local in that example) with:

autoreconf -i
make -j 4
sudo make install

You can, off course, install at your home directory (I usually put under $HOME/bin, or even $HOME/bin/jellyfish):

autoreconf -i
./configure --prefix=$HOME
make -j 4
make install

edit: the github releases page also provides compiled binaries for Linux and MacOsX.

ADD COMMENTlink modified 14 months ago • written 14 months ago by h.mon29k

Thanks a lot, I didn't realize that I was trying the first method which is meant for github releases. I did download one of those and then proceeded with ./configure...make install. It worked without giving any error, but now if I run jellyfish on my Terminal, it says 'command not found'. I would be happy to raise this as a separate question if you feel that is more appropriate, but if you have a quick suggestion for this, that would be awesome!

ADD REPLYlink written 14 months ago by c_u230

Use the path that you used at the configure step to the PATH environment variable. If you used --prefix=$HOME, then do:

ADD REPLYlink written 14 months ago by h.mon29k

OK. Actually export PATH=$path_I_used/bin:$PATH worked. For some reason, I had thought that one of the main jobs of make install was to add the path to the system path, but I guess not. Thanks a lot!

ADD REPLYlink written 14 months ago by c_u230

make install generally will do that if you have root access and are installing under that account.

ADD REPLYlink written 14 months ago by genomax83k
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