TOPHAT

This article gives a instruction of building the splice-junction tool TOPHAT, and the steps were extracted from TOPHAT home page plus my own experiences:

http://tophat.cbcb.umd.edu/tutorial.shtml#inst

Building TopHat from source

In order to build TopHat, you must have the following installed on your system: 

• the Boost C++ libraries (we recommend version 1.47 or higher so you can use it for Cufflinks as well) 
• the SAM tools library

Install Boost C++ libraries:

sudo apt-get install libboost-all-dev 
or
aptitude search boost
then use apt-get command to install the selected version. 

Install SamTools and setup:

1. Download the SAM tools
2. Unpack and cd to the SAM tools source directory.
3. Build the SAM tools with the command make at the command line. This also builds the library file libbam.a
4. Copy the samtools executable to a directory which is in your shell's PATH
5. Choose a base directory (prefix) where you want to have the ./lib/ and ./include/ subdirectories which will host the development files for the SAMTools API. A common choice is /usr/local, but if you don't have permissions to copy files under /usr/local/include and /usr/local/lib, you could choose another base directory (e.g. your home directory). Take note of this directory prefix because you will need to provide it to the --with-bam option of TopHat's ./configure script later.
6. Copy libbam.a to the ./lib/ subdirectory under the base (prefix) directory you've chosen above (e.g. cp *.a /usr/local/lib/)
7. Create a directory called "bam" under the ./include/ subdirectory in the base directory (e.g. mkdir /usr/local/include/bam/)
8. Copy the headers (files ending in .h) to the ./include/bam/ subdirectory you've just created above (e.g. cp *.h /usr/local/include/bam/)

Building TOPHAT:

Download: 
http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.tar.gz

1. Unpack the TopHat source tarball:

   tar zxvf tophat-2.0.9.tar.gz

2. Change to the TopHat directory:

   cd tophat-2.0.9

3. Configure TopHat using the ./configure script. If Boost libraries were installed somewhere other than under/usr/local, you will need to tell the installer where to find Boost using the --with-boost option, specifying the base (prefix) install directory for the Boost library as discussed in the Boost installation section above. In a similar fashion, to indicate the location of SAM tools development files, use the --with-bam option to the specify the base (prefix) directory which contains ./lib/libbam.a and ./include/bam as discussed above in the SAMTools installation section. The --prefix option specifies where TopHat programs will be installed, and it should point to a base directory path that will end up having a ./bin/ subdirectory containing the new TopHat programs. A common prefix choice can be, again, /usr/local, which will cause the final tophat program and binaries to be installed in /usr/local/bin/. 

          sudo ./configure --prefix=/usr/local

Finally, make and install TopHat.

    make

    make install