Skip to content

Installation

Jump to bottom Edit New page
hyattpd edited this page Aug 23, 2014 · 26 revisions

Prodigal consists of a single C executable which contains everything you need. Prodigal runs from the command-line (i.e. terminal window in Linux or MacOSX, or at the DOS command line in Windows). Binaries are provided with each release; however, you can also install the program other ways as described below.

Installing on Mac OS X

You can install on Mac OS X using homebrew or follow the instructions for the Generic Unix installation. To use the generic instructions, you will need to have XCode installed, which provides access to gcc and make.

To install using homebrew, first install homebrew. If already installed, make sure you have the latest version.

$ brew update

You will then need to tap into the prodigal repository.

$ brew tap hyattpd/prodigal
Cloning into '/usr/local/Library/Taps/hyattpd/homebrew-prodigal'...
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 6 (delta 0), reused 6 (delta 0)
Unpacking objects: 100% (6/6), done.
Checking connectivity... done.
Tapped 1 formula

Then you can install prodigal using the formula as follows:

$ brew install prodigal
==> Downloading https://github.com/hyattpd/Prodigal/archive/v2.6.1.tar.gz
######################################################################## 100.0%
==> make install
🍺  /usr/local/Cellar/prodigal/2.6.1: 4 files, 52K, built in 6 seconds

If you have a prodigal formula from another source, such as homebrew-science, you can use that (no guarantees it's up to date), or install explicitly from our tap with:

$ brew install hyattpd/prodigal/prodigal

Installing on Generic Unix

By "Generic Unix", we mean any system with gcc, make, and install. This includes MacOSX (BSD) and all flavors of Linux.

After you have uncompressed the source code, cd into the directory and do:

$ make install

This will install the prodigal binary in /usr/local/bin. If you wish to put it somewhere else, you can override the INSTALLDIR variable in the makefile.

$ make install INSTALLDIR=/where/i/want/prodigal/

Alternatively, you can just do:

$ make

to compile the executable in the current directory and then move it wherever you like.

Installing on Windows

The Windows binary should be the easiest option (available with each release).

If you do need to compile on Windows, though, you should use either Cygwin or MinGW. Once you have a terminal window with the basic commands like make, install, and gcc, follow the directions for Installing on Generic Unix.

Home * Introduction * Installation * Gene Prediction * By Input Type * Output Explained * Options Cheat Sheet * Next Steps * References

Clone this wiki locally