Problem in configuring TopHat

[genome1]

I am trying to analyze data generated from RNA-seq experiments. I am trying to align the RNA-Seq reads to the genome using TopHat. But, I have got struck while installing the TopHat! To begin with I have downloaded the following packages:
tophat-2.1.0.tar.gz
samtools-0.1.19.tar.bz2
boost_1_54_0.zip

I have unpacked all the packages.
For samtools: I have copied all C-header files in samtools-0.1.19/install/include/bam Then I copied the libbam.a file in samtools-0.1.19/install/lib

For boost: I have used the following commands:
$./bootstrap.sh
$./b2 install --prefix=PREFIX

For TopHat: I have used the command line:
$./configure --prefix=/path/to/tophat-2.1.0 --with-boost=/path/to/boost_1_54_0/PREFIX --with-bam=/path/to/samtools-0.1.19/install

But I am getting an error message. The last few lines of the error are as follows:
................
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
checking for boostlib >= 1.38.0... yes
checking for bamlib... yes
checking build system type... x86_64-unknown-linux-gnu
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... no
checking for exit in -lboost_thread... (cached) no
checking for exit in -lboost_thread... (cached) no
checking for exit in -llibboost_thread.a... no
configure: error: Could not link against libboost_thread.a !

Can anybody help me to identify the problem? What should be done to overcome this error. I have tried the same in both x86_64 Ubuntu system, but got the same error all the time!!

My 2nd query is that after my previous command when I try to use "make" command it shows:
make: *** No targets specified and no makefile found. Stop.

Is it due to not properly configuring the TopHat and hence not been able to create "makefile"?

[dpryan]

Why don't you just make your life easier and download the precompiled executable?

[genome1]

Hi dpryan,

Can you kindly tell me in details!

[dpryan]

Sure, you can just download the gzipped tar file here. Apparently they never precompiled 2.1.0, but I also don't see an update on the website about that.

BTW, "make" didn't work in your original post because the ./configure step failed (it makes the Makefile). That failed because it doesn't like something about the library path for boost. I'd have to quickly try to compile that locally to see if I can find out what's going wrong there.

[GenoMax]

Use this link to download the pre-compiled ready to run version: http://tophat.cbcb.umd.edu/downloads..._x86_64.tar.gz

It also appears to be available via ubuntu software center in 13.10. Not the latest version but close (2.0.8b).

[genome1]

Thanks dpryan and GenoMax, it is working now.