re-compile cufflinks

Cufflinks has offered binary file for download, which is very convenient and time-saving. The reason why I want to recompile cufflinks is: I found that cufflinks join reads with gap distance <50bp, and this is not adjustable for readers (at least in the current version).  But in some cases (e.g.. see below), you might want to adjust the gap threshold, esp. when you know they are from one gene/cluster. 

Here is steps I used to compile the cufflinks source code:

1. Install Boost

Remind: the new version might not work due to some version change issue (see here for more details). I used boost_1_45_0. 

cd ~/src

wget http://sourceforge.net/projects/boost/files/boost/1.45.0/boost_1_45_0.tar.gz/download

tar -zxvf boost_1_45_0.tar.gz

cd boost_1_45_0

./bootstrap.sh

./bjam --prefix=/home/dongx --toolset=gcc link=static runtime-link=static stage install

You can check the ~/bin/,  ~/lib/ and ~/include/ to see if the installation is successful. If success, there should be b2, bjam in the ~/bin, a list of libboost*.a files in ~/lib, and a ~/include/boost/ folder. 

2. Install Samtools (omit here)

3. Install cufflinks

# download, untar the file and cd the folder. 

[dongx@hpcc01 cufflinks-1.3.0]$ ./configure --prefix=/home/dongx/src/cufflinks-1.3.0 --with-boost=/home/dongx --with-bam=/home/dongx

When it's finished, you will see:

-- cufflinks 1.3.0 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread  -I/home/dongx//include
  GCC version:         gcc (GCC) 4.3.3
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /home/dongx/src/cufflinks-1.3.0
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <cole@cs.umd.edu> with questions and bug reports. 

[dongx@hpcc01 cufflinks-1.3.0]$make

[dongx@hpcc01 cufflinks-1.3.0]$make install