Issue during the make stage

CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data

http://csb5.github.io/lofreq/

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Issue during the make stage #110

Open Lakshay-sethi opened 3 years ago

Lakshay-sethi commented 3 years ago

I tried to run the make command while following the instructions from readme file. When I encountered this error:

#include "gsl/gsl_randist.h" not found

Is anyone else also facing this issue?

In order to combact it, I commented the following two lines in snpcaller.c #include "gsl/gsl_randist.h" #include "gsl/gsl_cdf.h"

andreas-wilm commented 3 years ago

Thanks for reporting. We've recently added a new feature (provided by the community) that depends on gsl. Apparently the build system doesn't ignore the absence of gsl headers properly. So I'll keep this issue open until it's fixed.

On a general node: unless you want to modify the source code I would recommend installing Lofreq via the precompiled binaries or via bioconda .

Andreas