compiling issues

[insilicool]

Following the instructions, I attempted to compile TMAP.

I was able to run the following:

git clone git://github.com/iontorrent/TMAP.git
cd TMAP
git submodule init

However, the git submodule update did not work give the following error:

error: RPC failed; result=22, HTTP code = 405
fatal: The remote end hung up unexpectedly
Unable to fetch in submodule path 'src/samtools'

Please help. Thanks!

Looks like Github is having trouble right now, I'm getting a timeout.

Also, be aware that this TMAP repository is no longer being updated. Life Technologies/Ion Torrent has moved TMAP development into the TS project.

More info here https://github.com/iontorrent/TMAP/wiki

Hey! I'm trying to compile TMAP according the instructions (clone from git && autogen.sh && ./configure && make), but when I run make, I got the following:

1.Several warning messages, about several Solutions in lib folder like this:

src/sw/lib/Solution7.cpp:556:36: warning: variable 'v_gap_ext' is uninitialized when used here [-Wuninitialized]
__m128i v_gap_ext; mm_set1_epi16(v_gap_ext, gap_extension);

2.And a fatal error:

src/sw/lib/Solution8.cpp:31:10: fatal error: 'ext/pool_allocator.h' file not found
#include <ext/pool_allocator.h>
^
2 warnings and 1 error generated.
make[2]: *** [src/sw/lib/Solution8.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Could someone figure it out what is happening?
Please help! Thanks!

[lvaruzza]

The library ext/pool_allocator.h was deprecated. In my experience you can just remove this line and the TMAP will compile.

I had this problems using the clang compiler in Mac OS, if you use the gcc-4.9 it compiles without problem.

Hi Ivaruzza!
I've set up a virtual machine to solve this problem and all works fine, but now I need to compile TMAP in my own computer (OS X 10.9.5) and I'm having problems with the clang compiler. I'm searching in tmap the line that specifies the compiler, so I can change to gcc (something like QMAKE_CC=gcc QMAKE_CXX=g++).
Could you help me with this? I must confess that install TMAP on Mavericks it's been at least confusing!

Thanks a lot!!!!!!

[ackd32]

I am having the exact same issue as delvaist, attempting to install TMAP on my laptop (OS X 10.11.1). I have very limited experience, so I'm uncertain how to go about removing the line relating to the library ext/pool_allocator.h, as suggested above:

"The library ext/pool_allocator.h was deprecated. In my experience you can just remove this line and the TMAP will compile."

Where do I look for the library ext/pool_allocator.h line? How do I go about opening up and modifying the file that contains it in the terminal?

I'm certain that this question must be very simple, but I am sure struggling with it.

[rayflowrc]

Hi delvaist,

I encountered the same problem when I tried to install TMAP on Mac OS. Would you please tell if you managed to compile TMAP. If yes can you give me some details (I am geneticist) ?