Can't install TopHat

[Trindade]

Hi,

I'm trying to install Tophat. I installed bowtie, samtools and boost (all they are ok, I think).
So, I do:

./configure --prefix=$HOME --with-boost=usr/include/boost --with-bam=$HOME/SAMTools

-- tophat 2.0.4 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -Iusr/include/boost/include -I/home/auri/SAMTools/include -I./SeqAn-1.3
Linker flags:
GCC version: gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Host System type: i686-pc-linux-gnu
Install prefix: /home/auri
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.

make

make all-recursive
make[1]: Entering directory `/home/auri/Downloads/tophat-2.0.4'
Making all in src
make[2]: Entering directory `/home/auri/Downloads/tophat-2.0.4/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/auri/Dowloads/boost_1_51_0/include -I/home/auri/SAMTools/include -I./SeqAn-1.3 -o segment_juncs -L/home/auri/Dowloads/boost_1_51_0/lib -L/home/auri/SAMTools/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/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4926: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4927: undefined reference to `boost::thread::~thread()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5003: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5004: undefined reference to `boost::thread::~thread()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
segment_juncs.o: In function `~thread_data':
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_data':
/usr/include/boost/thread/detail/thread.hpp:53: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o.rodata._ZTIN5boost6detail11thread_dataI19SegmentSearchWorkerEE[typeinfo for boost::detail::thread_data<SegmentSearchWorker>]+0x8): undefined reference to `typeinfo for boost::detail::thread_data_base'
collect2: ld returned 1 exit status
make[2]: ** [segment_juncs] Error 1
make[2]: Leaving directory `/home/auri/Downloads/tophat-2.0.4/src'
make[1]: ** [all-recursive] Error 1
make[1]: Leaving directory `/home/auri/Downloads/tophat-2.0.4'
make: ** [all] Error 2

I already tried two paths differents for boost on ./configure, but they finished with this same error when I do make.
--with-boost=usr/include/boost
--with-boost=$HOME/Downloads/boost_1_51_0


If someone can help me I would greatly appreciate it.

[kashidoc]

Same here.

I follow the instructions, and I came across the same problem. Have you found a solution, if you did, let me know. Thanks.

[Trindade]

Yep, I found.
Actually I tried something very simple and it worked: apt-get boost.
And don't specify the path for boost when you to configure the tophat, only for samtools.

./configure --prefix=/path/to/tophat_base_dir --with-bam=/path/to/libbam_prefix_dir
make
make install

[adamyao]

I had the same problem.
My boost 1.51.0 library was located in /home/adam/Downloads/lib
I did the following to solve the problem before installing TopHat:

LD_LIBRARY_PATH=/home/adam/Downloads/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH

[kashidoc]

Thank you.

The solution worked.

[MontseT]

Hi,

I am coming across a similar problem, but my error message is different (after doing "make" for tophat2):

boost::condition_variable::do_timed_wait(boost::unique_lock<boost::mutex>&, timespec const&)]+0xa1): undefined reference to `boost::system::system_category()'
collect2: ld returned 1 exit status
make[2]: *** [segment_juncs] Error 1
make[2]: Leaving directory `/home/uni05/mtorres/Programms/tophat-2.0.5/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/uni05/mtorres/Programms/tophat-2.0.5'
make: *** [all] Error 2

I think I have a problem linking the boost library to tophat, but I cannor figure out how to correctly do it.

For installing boost I did:

./b2 --prefix=$HOME/bin/ link=static runtime-link=static stage install

I tried adamyo's solution and didn't work. And I cannot use apt-get in the server I work with.

Any help will be incredibly welcome!

[Trindade]

Hi MontseT,

Do you tried build ./bjam?

[MontseT]

Yes, that was the first I tried, as TopHat instructions say so.
But while searching to solve the problem I found that, in boost, bjam has been in the last versions changed to b2.
I got the same result in both cases

[sudheer.svss]

how to set the prefix

[QUOTE=Trindade;85710]Yep, I found.
Actually I tried something very simple and it worked: apt-get boost.
And don't specify the path for boost when you to configure the tophat, only for samtools.

./configure --prefix=/path/to/tophat_base_dir --with-bam=/path/to/libbam_prefix_dir
make
make install[/QU
hi dear,
i m facing similar problem as u have metnioned in installing Tophat 2.0.6 , i have followed ur solution i.e typing apt-get boost ., but it showed unknown command. I have installed my boost in /usr/local as mentioned in the Tophat website., and ran just ./configure in Tophat ., and then make comand which gave the exact error as u have mentioned.
how to give the prefix imean path to tophat base dorectory ., as my pwd of tophat is root/NGS/tophat 2.0.6 and bam, i have saved it exactly as followed in the site., can u please write those prefixes instead of mentioning /path/to .. i am new to linux and I am struggling to install the Tophat., any suggestion ll help me in understanding the problem.,

[Trindade]

Do you tried sudo apt-get install boost and samtools is properly installed?
Maybe sudo apt-get install samtools can work too.

I think if you to install boost and samtools in your /usr/bin, tophat will found them by itself. But I don't know, it's just a idea.

[GenoMax]

hi dear,
i m facing similar problem as u have metnioned in installing Tophat 2.0.6 , i have followed ur solution i.e typing apt-get boost ., but it showed unknown command. I have installed my boost in /usr/local as mentioned in the Tophat website., and ran just ./configure in Tophat ., and then make comand which gave the exact error as u have mentioned.
how to give the prefix imean path to tophat base dorectory ., as my pwd of tophat is root/NGS/tophat 2.0.6 and bam, i have saved it exactly as followed in the site., can u please write those prefixes instead of mentioning /path/to .. i am new to linux and I am struggling to install the Tophat., any suggestion ll help me in understanding the problem.,

The prefixes would be given like this based on the info you have provided:

./configure --prefix=/NGS/tophat 2.0.6 --with-bam=/NGS/bam

I assume when you said root/NGS/tophat 2.0.6 that word root means "/NGS/tophat 2.0.6". If you truly have a directory called "root" at the top level then the prefixes would be

./configure --prefix=/root/NGS/tophat 2.0.6 --with-bam=/root/NGS/bam

Did you do

sudo apt-get libboost

to install the boost libraries

[sudheer.svss]

The prefixes would be given like this based on the info you have provided:

./configure --prefix=/NGS/tophat 2.0.6 --with-bam=/NGS/bam

I assume when you said root/NGS/tophat 2.0.6 that word root means "/NGS/tophat 2.0.6". If you truly have a directory called "root" at the top level then the prefixes would be

./configure --prefix=/root/NGS/tophat 2.0.6 --with-bam=/root/NGS/bam

Did you do

sudo apt-get libboost

to install the boost libraries

hi thanks a lot for ur suggestion., I have tried by entering command sudo apt-get libboost.,
but the error was bash :apt -get command not found ., and i have entered as a root user in my fedora 17.,

[GenoMax]

hi thanks a lot for ur suggestion., I have tried by entering command sudo apt-get libboost.,
but the error was bash :apt -get command not found ., and i have entered as a root user in my fedora 17.,

You are using Fedora 17.

I am not sure if the necessary package is available but you could try

yum install libboost

"yum" is the Fedora equivalent of "apt-get" (which is used for ubuntu etc).

If that does not work then:
Here is a link from the boost site for instructions to build and install: http://www.boost.org/doc/libs/1_53_0...library-binary