IDBA installation problem

Question

[kelvinfrog75]

I am trying to install IDBA for genome assembly. I downloaded the latest version IDBA 1.1.1 but when I try to install by ./configure and them make, I received the following error message and I don't think see the executable files in the bin folder

../src/container/hash_table.h:13:10: ****fatal error: ****'omp.h' file not found

Have anyone ever reported the similar problem? If so, can you give suggestion how to get around this problem. Thanks.

[h.mon]

The latest version is 1.1.2, found on IDBA github page. I can't reproduce the error with this version, you should try it. If it fails for you again, please provide more information, as exact commands used, operating system, gcc version.

[kelvinfrog75]

Hey, just to make sure, did you download the the IDBA from https://github.com/loneknightpy/idba, I downloaded it using the "DOWNLOAD ZIP" button. Is it how you download it?

[h.mon]

I downloaded from the releases page:

https://github.com/loneknightpy/idba/releases/download/1.1.2/idba-1.1.2.tar.gz

[kelvinfrog75]

I downloaded from the link you provide and I still get the same error. How do I check the gcc version? I used the same command lines that I used before, which is $ ./configure and then $ make. Thanks.

[kelvinfrog75]

Also, I used MAC to install this.

[kelvinfrog75]

Ok, here is the gcc version.

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)

Target: x86_64-apple-darwin13.4.0

Thread model: posix

Answer 1

[h.mon]

Try the suggestions from this or this StackOverflow posts.

This is a Mac specific problem, I can't help you more as I do not have a Mac. But apparently Clang (the default Mac compiler) does not have good OpenMP support, so you should install GCC with homebrew - additionally, homebrew has recipes for lots of bioinformatics applications.