I've been having some trouble installing a program called tophat on linux (here is a link to the installation guide http://tophat.cbcb.umd.edu/tutorial.html) and I was hoping you could help. It requires the boost libraries and another program called samtools to run, but both seemed to install fine, yet I'm getting an error from boost here. From what I see it seems to be that the boost libraries are not installed properly, specifically one to do with threads, I did some googling and went back and reinstalled them specifically stating to include the thread library but still no dice. Can anyone help?
This is the output of me running make.
make all-recursive
make[1]: Entering directory `/home/tuxedo/tophat-2.0.6'
Making all in src
make[2]: Entering directory `/home/tuxedo/tophat-2.0.6/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread - I../boost_1_52_0/boost.1.52.0//include -I../samtools_0.1.18//include -I./SeqAn-1.3 -o segment_juncs -L../boost_1_52_0/boost.1.52.0//lib -L../samtools_0.1.18//lib segment_juncs.o ../src/libtophat.a -lbam -lz
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4949: undefined reference to `boost::thread::join()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4950: undefined reference to `boost::thread::~thread()'
/home/tophat-2.0.6/src/segment_juncs.cpp:5026: undefined reference to `boost::thread::join()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:5027: undefined reference to `boost::thread::~thread()'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:4942: undefined reference to `boost::thread::thread(boost::function0<void, std::allocator<boost::function_base> > const&)'
/home/tuxedo/tophat-2.0.6/src/segment_juncs.cpp:5019: undefined reference to `boost::thread::thread(boost::function0<void, std::allocator<boost::function_base> > const&)'
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/home/tuxedo/tophat-2.0.6/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/tuxedo/tophat-2.0.6'
make: *** [all] Error 2
Thanks in advance for any help you can give!! This has been driving me crazy for hours now!!
