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Error when installing bedtools

Dear all, When I installed bedtools from the source, after using "make" command, it showed the error as below:

cc1plus: error: unrecognized command line option "-std=c++11"

make[1]: * [../../../obj//FileRecordMgr.o] Error 1

I guess the problem comes from gcc/g++ version. Currently, gcc version is 4.4.7. However, I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster. Could you suggest me some alternative ways to solve this problem? Thank you!

rna-seq bedtools gcc g++
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written by bobbyle0210 • bobbyle0210

I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster.

You can install your own gcc/g++ like any other program, can't you? Then you just direct make to use that one..

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written by 5heikki 5heikki

I cannot find the source to download gcc/g++. All guideline on the internet shows the use of sudo command. Could you give me some reference?

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written by bobbyle0210 • bobbyle0210

1 answer

Use pre-compiled binary available from GitHub repo for v.2.28.0. After downloading add execute permissions (chmod a+x ./bedtools).

Note: Latest bedtools version is 2.29.0 but no binary is available for that version.

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written by GenoMax GenoMax

Hi, thank you for your suggestion. But after this 2 steps, I still cannot run bedtools. It showed "command not found". What can I do now?

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written by bobbyle0210 • bobbyle0210

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