Error when installing bedtools

Question

[bobbyle0210]

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

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

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

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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!

[5heikki]

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..

[bobbyle0210]

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?

Answer 1

[GenoMax]

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.

[bobbyle0210]

Hi, Could you show more detailed steps for this, because I am not familar with linux yet? Should I follow this guideline:

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$ wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz

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$ tar -zxvf bedtools-2.28.0.tar.gz

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$ cd bedtools2

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$ make

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And where should I add execute permissions when following this guideline? Thanks so much!

[GenoMax]

What you downloaded is still the source code. You should instead do:

$ wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools
$ chmod a+x ./bedtools

This file is pre-compiled binary which is ready to run after the two steps above.

[bobbyle0210]

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?

[WouterDeCoster]

The bedtools binary should be in your $PATH.
See also this page