I am trying to compile somatic sniper from source but run into compilation errors.
I cloned the git repository yesterday
$ git clone --recursive git://github.com/genome/somatic-sniper.git
ran cmake
$ cmake ../somatic-sniper/ -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done No CMAKE_BUILD_TYPE specified, defaulting to release SAMTOOLS_ROOT is set to: /Users/xxx/samtools-0.1.16 -- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.3") -- Found Samtools - Samtools include dirs: /Users/xxx/samtools-0.1.16;/usr/include - Samtools libraries: /Users/xxx/samtools-0.1.16/libbam.a;/usr/lib/libz.dylib -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY) Google Test framework not found, no tests will be built GTest is available at http://code.google.com/p/googletest/ Ubuntu users can likely sudo apt-get install gtest -- Configuring done -- Generating done -- Build files have been written to: /Users/xxx/SomaticSniper
and finally make
$ 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 [ 30%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_bed.c.o [ 40%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_classic.c.o [ 50%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_format.c.o [ 60%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_vcf.c.o [ 70%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_maqcns.c.o [ 80%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_pileup.c.o /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c: In function ‘bam_plbuf_reset’: /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:124: error: ‘bam_plbuf_t’ has no member named ‘max_tid’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:124: error: ‘bam_plbuf_t’ has no member named ‘max_pos’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:125: error: ‘bam_plbuf_t’ has no member named ‘tid’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:125: error: ‘bam_plbuf_t’ has no member named ‘pos’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:126: error: ‘bam_plbuf_t’ has no member named ‘is_eof’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:127: error: ‘bam_plbuf_t’ has no member named ‘head’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:129: error: ‘bam_plbuf_t’ has no member named ‘mp’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:132: error: ‘bam_plbuf_t’ has no member named ‘head’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:132: error: ‘bam_plbuf_t’ has no member named ‘tail’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c: In function ‘bam_plbuf_set_mapq_thresh’: /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:137: error: ‘bam_plbuf_t’ has no member named ‘mapq_thresh’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:138: error: ‘bam_plbuf_t’ has no member named ‘mapq_thresh’ [... and many similar ones ...] make[2]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_pileup.c.o] Error 1 make[1]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/all] Error 2 make: *** [all] Error 2
There seems to be a conflict between struct __bam_plbuf_t in sniper_pileup.c and samtool's bam.h
typedef struct {
bam_plp_t iter;
bam_pileup_f func;
void *data;
} bam_plbuf_t;
but I don't know how to solve it.
Any suggestions?
1 answer
SomaticSniper requires samtools v0.1.6. It looks like you are trying to link to samtools 0.1.16 and thus you are getting the conflicts.
When I run "make", I get the following errors:
Scanning dependencies of target sniper [ 10%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/alleleutil.c.o [ 20%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/dqstats.c.o [ 30%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/outputbed.c.o [ 40%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/outputclassic.c.o [ 50%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/outputformat.c.o [ 60%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/outputvcf.c.o [ 70%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/snipermaqcns.c.o In file included from /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.c:4: /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.h:5:17: error: glf.h: No such file or directory In file included from /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.c:4: /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.h:26: error: expected â=â, â,â, â;â, âasmâ or âattributeâ before ââ token /home/Tools/somatic-sniper/src/lib/sniper/sniper_maqcns.h:27: warning: type defaults to âintâ in declaration of âglf1_tâ /home/Tools/somatic-sniper/src/lib/sniper/sniper_maqcns.h:27: error: expected â;â, â,â or â)â before ââ token /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.h:29: warning: type defaults to âintâ in declaration of âglf1tâ /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.h:29: error: expected â;â, â,â or â)â before â*â token /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.c:127: error: expected â=â, â,â, â;â, âasmâ or âattributeâ before ââ token /home/Tools/somatic-sniper/src/lib/sniper/sniper_maqcns.c:250: warning: type defaults to âintâ in declaration of âglf1_tâ /home/Tools/somatic-sniper/src/lib/sniper/sniper_maqcns.c:250: error: expected â;â, â,â or â)â before ââ token /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.c:275: warning: type defaults to âintâ in declaration of âglf1tâ /home/Tools/somatic-sniper/src/lib/sniper/snipermaqcns.c:275: error: expected â;â, â,â or â)â before â*â token make[2]: * [build/src/lib/sniper/CMakeFiles/sniper.dir/snipermaqcns.c.o] Error 1 make[1]: [build/src/lib/sniper/CMakeFiles/sniper.dir/all] Error 2 make: ** [all] Error 2
What does this mean?? Thanks, Rini
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