Basic question about using ./configure for installing a software
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2.7 years ago
c_u ▴ 480

Hi,

This is a naive question. I am trying to install Jellyfish (http://www.genome.umd.edu/jellyfish.html) on a Mac. For that, their docs say (https://github.com/gmarcais/Jellyfish#installation) -

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 configure.ac. Could someone let me know what is the mistake I am committing? Thanks!! installation jellyfish • 755 views ADD COMMENT 3 Entering edit mode 2.7 years ago h.mon 33k 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 ./configure 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.

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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!

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Use the path that you used at the configure step to the PATH environment variable. If you used --prefix=$HOME, then do: export PATH=$HOME:$PATH  ADD REPLY 0 Entering edit mode OK. Actually export PATH=$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!

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