bahlolab / superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.

GNU General Public License v2.0

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fatal error: kseq.h: No such file or directory #4

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

Hi I am trying to install superstr but getting the foll. error when running cmake . && make-

Scanning dependencies of target superstr [ 8%] Building C object CMakeFiles/superstr.dir/main.c.o softwares/superSTR/C/main.c:8:18: fatal error: kseq.h: No such file or directory

include

compilation terminated. make[2]: [CMakeFiles/superstr.dir/build.make:83: CMakeFiles/superstr.dir/main.c.o] Error 1 make[1]: [CMakeFiles/Makefile2:96: CMakeFiles/superstr.dir/all] Error 2 make: *** [Makefile:104: all] Error 2

lfearnley commented 3 years ago

Hi @hchetia!

This is an error where superSTR isn't finding the path to your htslib install. You'll need to set the HTSLIB_ROOT environment variable in your shell to be the path to the htslib libraries using something like export HTSLIB_ROOT=<your path here>.

The only potential issue that I'm aware of with this is that sometimes there can be some issues with module systems (commonly found in HPC systems); if you're using a copy of htslib that has been installed through this, make sure you module load the htslib when using superSTR.

hchetia commented 3 years ago

Hi @lfearnley I followed your advice and superSTR installed successfully. Thanks.