Tool: IDBA installation problem
0
gravatar for kelvinfrog75
4.7 years ago by
kelvinfrog7510
kelvinfrog7510 wrote:

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 excusable 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.

tool assembly • 2.7k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by kelvinfrog7510

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.

ADD REPLYlink written 4.7 years ago by h.mon31k

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?

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by kelvinfrog7510

I downloaded from the releases page:

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

ADD REPLYlink written 4.7 years ago by h.mon31k

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.

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by kelvinfrog7510

Also, I used MAC to install this.

ADD REPLYlink written 4.7 years ago by kelvinfrog7510

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

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by kelvinfrog7510
0
gravatar for h.mon
4.7 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by h.mon31k
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