grabix installation from github

Question

[jonessara770]

Hello,

I downloaded grabix from github but dont kow how to make executable or install? Please advice

https://github.com/arq5x/grabix

Thanks

[GenoMax]

It is customary to provide a link for the tool you are referring to with these type of posts. There can be multiple programs with same/similar names. Please add that information to your original post.

[WouterDeCoster]

It's probably more appropriate to open an issue on GitHub.

I see a Makefile so my first guess would be make.

But I would always suggest to install from (bio)conda.

[jonessara770]

Thanks

when running make I get this error

gcc -Wall -O2 -o grabix grabix_main.cpp grabix.cpp bgzf.c -lstdc++ -lz
/tmp/ccPts8pX.s: Assembler messages:
/tmp/ccPts8pX.s:21: Error: expecting string instruction after `rep'
/tmp/ccPts8pX.s: Assembler messages:
/tmp/ccPts8pX.s:1036: Error: expecting string instruction after `rep'
/tmp/ccPts8pX.s:1245: Error: expecting string instruction after `rep'
make: *** [all] Error 1

[GenoMax]

What OS are you compiling on? What version of gcc and binutils?

[jonessara770]

CentOS6/software/gcc/gcc-4.9.3/bin/gcc

[GenoMax]

I was able to compile on RHEL with gcc 4.8.x. So you should be able to.

What do you see with ld -v?

What about using the bioconda method suggested by @Wouter?

[GenoMax]

Tagging: brentp

Answer 1

[jonessara770]

Ok I unloaded module file gcc-4.9.3 and run 'make' it and it create grabix

[GenoMax]

Great. Then we are done!