Somatic Sniper Compilation Issues

Question

[nakavthekar]

Hi, I was hoping to compile somatic-sniper but I received some issues:

$ make
Scanning dependencies of target sniper
[ 10%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/allele_util.c.o
[ 20%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/dqstats.c.o
In file included from /home/user/somatic-sniper/src/lib/sniper/dqstats.c:1:0:
/home/user/somatic-sniper/src/lib/sniper/dqstats.h:5:17: fatal error: bam.h: No such file or directory
compilation terminated.
make[2]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/dqstats.c.o] Error 1
make[1]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/all] Error 2
make: *** [all] Error 2

I'm using samtools v0.1.6 but I've noticed that the bam file is properly contained in the newest version of samtools. Please let me know if I'm blatantly overlooking something or if I'm missing a build requirement of some sort.

Thanks so much in advance.

[Eric Normandeau]

Have you tried copying or linking the bam.h file into the directory where it is expected (may be evident from the dqstats.c.o file)?

[Poduval]

I have tried all the given guide lines to install somatic sniper on my Mac OSX 10.9.2. but when I do

make -j

I get these errors

/Users/krsna/tools/Final_Cake/software_path/somatic-sniper/src/lib/sniper/dqstats.h:5:10: ****fatal error: ****'bam.h' file not found**

#include <bam.h>
**         ^**
**/Users/krsna/tools/Final_Cake/software_path/somatic-sniper/build/vendor/src/gtest160/include/gtest/internal/gtest-port.h:499:13: ****fatal error: ****'tr1/tuple' file not found**
#   include <tr1/tuple>  // NOLINT
**            ^**
1 error generated.
make[5]: *** [CMakeFiles/gtest.dir/src/gtest-all.cc.o] Error 1
make[4]: *** [CMakeFiles/gtest.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [vendor/src/gtest160-stamp/gtest160-build] Error 2
make[1]: *** [CMakeFiles/gtest160.dir/all] Error 2
make: *** [all] Error 2

Can you please help me with this.

Thank you.

Regards,
Deepak

Answer 1

[tgi.tabbott]

Hello. Please make sure you export the environment variable SAMTOOLS_ROOT to point to the directory where you compiled samtools. This directory should contain bam.h as well as libbam.a. You may need to remove the contents of your build directory and rerun cmake after doing so as it could be caching an incorrect path to where it thinks samtools is.

If you still have problems, show us the output of cmake. Of particular interest are the lines mentioning the path where it thinks it found samtools:

...
SAMTOOLS_ROOT is set to: /gsc/pkg/bio/samtools/samtools-0.1.6
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.3.3") 
-- Found Samtools 
 - Samtools include dirs: /gsc/pkg/bio/samtools/samtools-0.1.6;/usr/include
 - Samtools libraries: /gsc/pkg/bio/samtools/samtools-0.1.6/libbam.a;/usr/lib/libz.so
...