I tried to install the tophat 2.0.0 using source code on my redhat linux ES5 machine by following the instructions at
http://tophat.cbcb.umd.edu/manual.html. Everything (Bowtie2, Boost-1.49, Samtools-0.1.18) went well until I tried to run make on tophat. The error message is as follows:
"g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/gpfs/home/zuz17/bin//include -I/gpfs/home/zuz17/bin//include -I./SeqAn-1.3 -o prep_reads -L/gpfs/home/zuz17/bin//lib prep_reads.o ../src/libtophat.a -lbam -lz -lz
/gpfs/home/zuz17/bin//lib/libbam.a(razf.o): In function `razf_open_w':
/gpfs/home/zuz17/tools/samtools-0.1.18/razf.c:186: undefined reference to `deflateSetHeader'
collect2: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[2]: Leaving directory `/gpfs/home/zuz17/tools/tophat-2.0.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/gpfs/home/zuz17/tools/tophat-2.0.0'
make: *** [all] Error 2
"
I have already installed zlib (1.2.3) because running 'locate zlib.h' gave
/usr/include/bzlib.h
/usr/include/zlib.h
/usr/include/boost/iostreams/detail/config/zlib.hpp
/usr/include/boost/iostreams/filter/zlib.hpp
/usr/lib/syslinux/com32/include/zlib.h
Please help to figure out what I should do to fix this problem. Thank you.
Best wishes!
Zhenguo
http://tophat.cbcb.umd.edu/manual.html. Everything (Bowtie2, Boost-1.49, Samtools-0.1.18) went well until I tried to run make on tophat. The error message is as follows:
"g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/gpfs/home/zuz17/bin//include -I/gpfs/home/zuz17/bin//include -I./SeqAn-1.3 -o prep_reads -L/gpfs/home/zuz17/bin//lib prep_reads.o ../src/libtophat.a -lbam -lz -lz
/gpfs/home/zuz17/bin//lib/libbam.a(razf.o): In function `razf_open_w':
/gpfs/home/zuz17/tools/samtools-0.1.18/razf.c:186: undefined reference to `deflateSetHeader'
collect2: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[2]: Leaving directory `/gpfs/home/zuz17/tools/tophat-2.0.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/gpfs/home/zuz17/tools/tophat-2.0.0'
make: *** [all] Error 2
"
I have already installed zlib (1.2.3) because running 'locate zlib.h' gave
/usr/include/bzlib.h
/usr/include/zlib.h
/usr/include/boost/iostreams/detail/config/zlib.hpp
/usr/include/boost/iostreams/filter/zlib.hpp
/usr/lib/syslinux/com32/include/zlib.h
Please help to figure out what I should do to fix this problem. Thank you.
Best wishes!
Zhenguo