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"?
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"?
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