Cannot compile Lumpy-SV.

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2.7 years ago

Ishak ▴ 20

Dear Biostars

I try to download lumpy-sv by using these steps :

git clone --recursive https://github.com/arq5x/lumpy-sv.git

cd lumpy-sv

make

after make I get that

cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl

checking for gcc... gcc

checking whether the C compiler works... no

configure: error: in `/home/gnks/Desktop/Temp_yusuf_baran/clincv38_v2/lumpy-sv/lib/htslib':

configure: error: C compiler cannot create executables

See `config.log' for more details

Makefile:74: recipe for target 'htslib' failed

make: *** [htslib] Error 77

Any suggestion?

By the way I try to install KCCG / ClinSV

structural KCCG ClinSV variation • 1.2k views

ADD COMMENT • link 2.7 years ago by Ishak ▴ 20

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it's not a problem with lumpy, it's a problem with your server:

checking whether the C compiler works... no

check gcc is available and functional.

ADD REPLY • link 2.7 years ago by Pierre Lindenbaum 161k

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They provide both Docker and Singularity images which are basically fixed containers that include all required software and the tool itself. It is simple to use, just follow the instructions at the link below, that saves you from any compilation because there is indeed lots of stuff to setup for this tool: https://github.com/KCCG/ClinSV#run-clinsv

You will need to install Docker on your system.

ADD REPLY • link 2.7 years ago by ATpoint 82k

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yes, they provide docker and singularity only with ref genome 37 and I work on hg 38.

ADD REPLY • link 2.7 years ago by Ishak ▴ 20

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