How to Install EasyCodeML on OSX

Question

[kacollier]

I'm wanting to test for selection on a set of aligned genes, and codeml looked like a good place to start. The program EasyCodeML (https://github.com/BioEasy/EasyCodeML) is a wrapper for the core codeml program, but the Github distribution is very vague on how to actually install it and get it to run.

Currently, the EasyCodeML-master file is in my Documents. I was able to find the .jar file easily, but when I try to launch it from Finder, it gives two errors. The first one says 'Can't found 'codeml.exe' or 'chi2.exe', and the second one says 'Could NOT found the Custom Files in the same directory of EasyCodeML.jar.'

There are a set of chi2.exe and codeml.exe files in a folder labeled 'Mac', and I assume I need to do something to install the program, but I''m confused as to what that is. Any help would be appreciated.

[Ram]

.exe. files are executable files for Windows. Opening the jar file from Finder is not a great idea - try running it from the command line: java -jar /path/to/EasyCodeML.jar. If it errors out, paste the command and error in a new GiitHub issue on their repository.

[kacollier]

Okay, that worked- thanks for the tip!

Answer 1

[Biodeer]

Glad to know you solve it. For others who search the EasyCodeML (https://github.com/BioEasy/EasyCodeML), EasyCodeML is written in Java. Precompiled versions are available for Microsoft Windows, Mac OS X, and Linux. Before running EasyCodeML, please ensure that your computer has a recent version of the Java Runtime Environment (JRE 1.6 or higher).