Tool:IDBA installation problem
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6.0 years ago
kelvinfrog75 ▴ 10

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.

Assembly Tool • 3.2k views
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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.

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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?

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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.

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Also, I used MAC to install this.

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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

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6.0 years ago
h.mon 33k

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.

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