Install Mugsy On Mac Os X (10.6)

Question

[Whetting]

Hi Biostars,
I am trying to install Mugsy on mac os x. I am having a really hard time to compile it...
The make commaned gives me 100's of errors.

synchain-mugsy.cpp:86:36: error: boost/graph/graphviz.hpp: No such file or directory synchain-mugsy.cpp:87:42: error: boost/graph/adjacencylist.hpp: No such file or directory synchain-mugsy.cpp:88:44: error: boost/graph/adjacencymatrix.hpp: No such file or directory synchain-mugsy.cpp:89:35: error: boost/unordered_set.hpp: No such file or directory

...

field ‘printlabel’ declared void graph.h:380: error: ‘OrientedLabelSet’ was not declared in this scope graph.h:380: error: ‘i’ was not declared in this scope make[1]: * [synchain-mugsy.o] Error 1 make: * [synchain_mugsy] Error 2

has anyone successfully compliled on a mac? any help would be appreciated!

Answer 1

[Matt Shirley]

It looks like you need the boost development libraries. If you are using MacPorts, you can do

sudo port install boost

[Whetting]

thanks, Seems like I am missing all kind of dependencies. Most of them I am unable to install. gpgme seems the hardest nut to crack

[Matt Shirley]

I am running Mac OS 10.8, and just tried downloading the Mugsy sources. I have all the correct development libraries, and it still refuses to build. There is little hope for trivially producing a native Mac binary at this time.

[Whetting]

ok, thanks for giving it a shot...

Answer 2

[Whetting]

I think part of the problem is this:

g++ -I /usr/local/projects/angiuoli/boost/include/boost-138 -pedantic -ftemplate-depth-200 -DLARGEFILESOURCE -DFILEOFFSETBITS=64 -O3 synchain-mugsy.cpp -static -I /usr/local/projects/angiuoli/boost/include/boost-1_38 -c -o synchain-mugsy.o synchain-mugsy.cpp:86:36: error: boost/graph/graphviz.hpp: No such file or directory

the usr/local/projects/angiuoli/boost refers to the person who developed Mugsy (Dr. Angiuoli). I will have to edit the make file.

[hillary.figler]

Did you ever figure out how to edit this part?

Answer 3

[Cliff Beall]

I have set it up with VirtualBox and Ubuntu 10.04 and the pre-compiled mugsy (x86-64-v1r2.1), on a Mac running 10.6. I have not done a whole lot with it yet, but it runs.

[Whetting]

@Cliff, you use the precompiled version on Mac? Or did you compile it?

[Cliff Beall]

The precompiled version. I did set up a Linux virtual machine but that is free and not too hard to get going.

I can't remember if I tried the precompiled natively in MacOS, but most times that sort of thing doesn't work.

[Whetting]

why did you setup an Ubuntu virtual machine? Mac os x 10.6 is supposed to be "linux". I guess that is a possibility though...

[Matt Shirley]

Mac OS is not linux. Mac OS runs a Mach) kernel, while the Linux kernel is something totally different (simplified version: they run programs in different "levels", and with different paradigms). The kernel interfaces with your computer's hardware, and is therefore called upon when you execute a program to translate the program's instructions to something your computer can understand. When people talk about "linux", they are generally speaking of the linux kernel, plus all of the programs that run on top of it. These programs must be compiled specifically for the kernel and associated other programs that make up your operating system. Sometimes people refer to Mac OS as being Unix based. This is true, but it does not extend to allowing binary compatibility between all Unix operating systems. You wouldn't think that you can take Ford engine parts and put them in a Ferrari as-is. Even programs compiled under a different compiler version (GCC for C) may refuse to run on the same operating system, if the OS version is significantly older or newer.