Question: Compiling Somatic Sniper -- Can'T Find Glf.H
0
gravatar for Jeremy Schwartzentruber
5.7 years ago by
Wellcome Trust Sanger Institute, Cambridge, UK

Hello. I am trying to install somatic sniper on a linux cluster (CentOS), but I can't get past one build issue. (I've searched Biostar, Seqanswers, Google... and can't find any help.) It seems that it can't find file glf.h. Is this part of some package I should have installed already?

I get the following error:

[jschwart@lg-1r14-n04 somatic-sniper]$ make [ 40%] Built target gtest160 [ 45%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_maqcns.c.o In file included from /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:4: /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:5:17: error: glf.h: No such file or directory

In file included from /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:4: /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:26: error: expected â=â, â,â, â;â, âasmâ or â__attribute__â before ââ token /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:27: warning: type defaults to âintâ in declaration of âglf1_tâ /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:27: error: expected â;â, â,â or â)â before ââ token /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:29: warning: type defaults to âintâ in declaration of âglf1_tâ /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.h:29: error: expected â;â, â,â or â)â before ââ token /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:127: error: expected â=â, â,â, â;â, âasmâ or â__attribute__â before ââ token /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:250: warning: type defaults to âintâ in declaration of âglf1_tâ /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:250: error: expected â;â, â,â or â)â before ââ token /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:275: warning: type defaults to âintâ in declaration of âglf1_tâ /...mypath/somatic-sniper/src/lib/sniper/sniper_maqcns.c:275: error: expected â;â, â,â or â)â before ââ token make[2]: ** [build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_maqcns.c.o] Error 1 make[1]: ** [build/src/lib/sniper/CMakeFiles/sniper.dir/all] Error 2 make: *** [all] Error 2

Cmake ran successfully, and reported that it was finding samtools version 0.1.6. Any help would be greatly appreciated. Thanks!

Jeremy

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ADD COMMENTlink written 5.7 years ago by Jeremy Schwartzentruber20
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