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Old 09-18-2012, 09:03 AM   #1
Trindade
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Default Can't install TopHat

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 <cole@cs.umd.edu> 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.
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Old 10-02-2012, 07:02 AM   #2
kashidoc
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Default 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.
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Old 10-04-2012, 04:08 PM   #3
Trindade
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Default

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
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Old 10-04-2012, 11:48 PM   #4
adamyao
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Default

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
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Old 10-05-2012, 06:01 AM   #5
kashidoc
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Default Thank you.

The solution worked.
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Old 10-24-2012, 05:47 AM   #6
MontseT
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Default

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!
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Old 10-24-2012, 10:08 AM   #7
Trindade
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Default

Hi MontseT,

Do you tried build ./bjam?
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Old 10-24-2012, 11:46 AM   #8
MontseT
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Default

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
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Old 02-18-2013, 11:39 PM   #9
sudheer.svss
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Default 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.,
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Old 02-19-2013, 03:07 AM   #10
Trindade
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Default

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.
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Old 02-19-2013, 03:19 AM   #11
GenoMax
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Default

Quote:
Originally Posted by sudheer.svss View Post
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

Code:
sudo apt-get libboost
to install the boost libraries
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Old 02-19-2013, 03:32 AM   #12
sudheer.svss
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Question

Quote:
Originally Posted by GenoMax View Post
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

Code:
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.,
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Old 02-19-2013, 03:42 AM   #13
GenoMax
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Default

Quote:
Originally Posted by sudheer.svss View Post
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

Code:
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
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