Help Contributing to Mothur's Source

I want to extend the functionality of Mothur’s Classify.Seqs module, and if my new tools work well contribute them to the community. However, I’m new to both Github and contributing to Open Source projects in general, so I wanted to reach out to the developers and the community and see what everyone uses to do their development with.

My coworkers suggested I use Eclipse, which has a built-in module for interfacing with GitHub, but as a long-time programmer in VI, it’s all a bit overwhelming. Suggestions for what IDE to use and how to get started would be greatly appreciated.


Everything we do is in Xcode, but you’re more than willing to contribute. We’ll be in touch on the details.

I’ve having occasional problems compiling Mothur from source. The crux of the problem is these two lines in mothur.cpp’s main():
string temp = MOTHUR_FILES;
which throws an error saying the second line isn’t valid.

MOTHUR_FILES is set by the user in the makefile, and passed in to the compiler like so:
g++ blah blah –DMOTHUR_FILES=”/my_directory/” blah blah blah

Which caused the one copy I’ve got successfully compiled to replace MOTHUR_FILES with the value I passed in:
string temp = “/my_directory/”;

But I can’t get that to happen consistently - most of the time it remains “MOTHUR_FILES” and so I’m currently hard-coding it in the source. Any suggestions for what’s going on? When/How is the C pre-processor substituting the value of MOTHUR_FILES for it’s token?

For the record I’m working from a linux server running Ubuntu 10.04, and compiling with the GNU C++ compiler.


We haven’t seen that error before. What version of the compiler are you using?

g++ (Ubuntu 4.4.3-4ubuntu5) 4.4.3

What’s most confusing to me is that it’s worked before. It seems to primarily be an issue when compiling from within my IDE (Eclipse), despite the fact that it’s just calling make the same way I did.