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Cannot link TopHat against libboost_thread.a

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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 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 !

Now my question is why I am getting the error message and what can be done to overcome this. I have tried the same in both x86_64 Ubuntu systems, but got the same error all the time!


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