hi dears,
i am trying to install Tophat 2.0.0 in fedora 17. I have installed boost in usr/local/include. and downloaded samtools 0.1.18, copied libbam.a to usr/local/lib and .h files in to usr/local/include/bam.
I have copied the the executable files like bcftools, misc to usr/local/bin as mentioned., but I am not able to find samtools executables that are to be copied to usr/local/bin in the samtools 0.1.18.
i have run the make command in Tophat 2.0.0 and the error is
make all-recursive
make[1]: Entering directory `/root/NGS/tophat-2.0.0'
Making all in src
make[2]: Entering directory `/root/NGS/tophat-2.0.0/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lbam -lz -lz
/usr/bin/ld: segment_juncs.o: undefined reference to symbol '_ZN5boost6system15system_categoryEv'
/usr/bin/ld: note: '_ZN5boost6system15system_categoryEv' is defined in DSO /usr/local/lib/libboost_system.so.1.53.0 so try adding it to the linker command line
/usr/local/lib/libboost_system.so.1.53.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/root/NGS/tophat-2.0.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/NGS/tophat-2.0.0'
make: *** [all] Error 2
please help me in this regard., as I am new to these installation steps I am not figureout the cause of error.
i am trying to install Tophat 2.0.0 in fedora 17. I have installed boost in usr/local/include. and downloaded samtools 0.1.18, copied libbam.a to usr/local/lib and .h files in to usr/local/include/bam.
I have copied the the executable files like bcftools, misc to usr/local/bin as mentioned., but I am not able to find samtools executables that are to be copied to usr/local/bin in the samtools 0.1.18.
i have run the make command in Tophat 2.0.0 and the error is
make all-recursive
make[1]: Entering directory `/root/NGS/tophat-2.0.0'
Making all in src
make[2]: Entering directory `/root/NGS/tophat-2.0.0/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/local/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lboost_thread -lbam -lz -lz
/usr/bin/ld: segment_juncs.o: undefined reference to symbol '_ZN5boost6system15system_categoryEv'
/usr/bin/ld: note: '_ZN5boost6system15system_categoryEv' is defined in DSO /usr/local/lib/libboost_system.so.1.53.0 so try adding it to the linker command line
/usr/local/lib/libboost_system.so.1.53.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/root/NGS/tophat-2.0.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/NGS/tophat-2.0.0'
make: *** [all] Error 2
please help me in this regard., as I am new to these installation steps I am not figureout the cause of error.
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