Question: Error downloading MuSiC2
gravatar for banerjeeshayantan
7 months ago by
banerjeeshayantan80 wrote:

I am following all the steps that are required to install music2. I am trying to download calcRoiCovg in one of the steps. I have followed all the instructions previously, but I am getting the following error.

    gcc -g -Wall -fopenmp -O2 -Idata/shayantan/samtools/ calcRoiCovg.c -o calcRoiCovg -Ldata/shayantan/samtools/ -lbam -lm -lz -lpthread In file included from calcRoiCovg.c:21:0:  calcRoiCovg.h:22:17: fatal error: sam.h: No such file or directory  #include "sam.h"    ^   compilation terminated.   make: *** [all] Error 1

I have made sure that sam.h file is inside samtools and htslib. But still I get an error. Any suggestions to remedy this will help me a lot! I am stuck with this problem for a long time.

ADD COMMENTlink modified 7 months ago by genomax64k • written 7 months ago by banerjeeshayantan80
gravatar for genomax
7 months ago by
United States
genomax64k wrote:

That is not an error with downloading MuSiC2 but a problem with compilation. You need to make sure that you have the directory containing samtools and htslib added to your $PATH.

export PATH=$PATH:/directory_with_samtools

ADD COMMENTlink written 7 months ago by genomax64k
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