TransBorrow安装

1.boost安装

 1. Installing Boost

    a) download a version of boost and unpack it

       $ tar zxvf boost_1_47_0.tar.gz

    b) change to the boost directory and run ./bootstrap.sh

       $ cd boost_1_47_0
       $ ./bootstrap.sh

    c) run

       $ ./b2 install --prefix=<YOUR_BOOST_INSTALL_DIRECTORY>

       For example, if you want install boost in /home/juntaosdu/local/boost, the command is :
      
       $ ./b2 install --prefix=/home/spider/project/yuantao/soft/boost_1_74_0/boost

       If the boost is installed successfully, you would find two sub-directories 
       in /home/spider/project/yuantao/soft/boost_1_74_0/boost:

       /home/spider/project/yuantao/soft/boost_1_74_0/boost/include/
       /home/spider/project/yuantao/soft/boost_1_74_0/boost/lib/

      Note: The default Boost installation directory is /usr/local. Take note of the boost 
      installation directory, because you need to tell the TransBorrow installer where to find 
      boost later on.

      (WARNING: The paths of "boost/lib/" and "boost/include/" should be added to the 
      CMakeList.txt of TransBorrow in TransBorrow_v.1.1/src/ later on.)

2.Bamtools安装

2. Installing BamTools
  
   a) change to the bamtools directory and make a new directory named "build"

      $ cd TransBorrow_v.1.1/bamtools
      $ mkdir build
      $ cd build

   b) type cmake and make it install

      $ cmake ../
      $ make

     Note: Go back up to the BamTools root directory. 
     
     1) Assuming the build process finished correctly, you should be able to find 
     the toolkit executable here:
     
     ./bin/
     
     2) The BamTools API and Utils libraries will be found here:
     
     ./lib/
     
     3) The BamTools API headers will be found here:
     
     ./include/*

     (WARNING: The paths of ./lib/ and ./include/ should be added to the CMakeList.txt 
     of TransBorrow in TransBorrow_v.1.1/src/ later on.)

3.TransBorrow安装

 Building TransBorrow

      a) unpack the TransBorrow and change to the TransBorrow directory

       $ tar zxvf TransBorrow_v.1.1.tar.gz
       $ cd TransBorrow_v.1.1


      c) Add the lib and include paths of boost and bamtools to the CMakeList.txt 
      of TransBorrow in TransBorrow_v.1.1/src/CMakeList.txt
    
      (Note: The file CMakeList.txt will guide you how to add these two paths. Please read 
      lines 7, 9, 11, 13, 15 in CMakeList.txt for the approach of adding these two paths.)

      d) change to the TransBorrow root directory and make a new directory named "build"

       $ cd TransBorrow_v.1.1
       $ mkdir build
       $ cd build

      e) type the cmake and make commands for final building TransBorrow

       $ cmake ../src
       $ make
 

4.获取转录本

~/project/yuantao/soft/TransBorrow_v.1.1/build/TransBorrow -r trans.stringtie.gtf -g /home/spider/project/yuantao/test/17_T_ant/Trichonephila_antipodiana.fa -b map.rna.bam -s unstranded -t 40