How to rectify issues occurring while installing Cufflinks and Boost?

I'm having a problem installing Cufflinks. Before installing Cufflinks, I installed Boost first with:

bjam --prefix=/Users/jimmy/Downloads/boost_1_46_1/ toolset=gcc link=static install

It seems to be ok.

However, when installing Cufflinks, it seems there is a problem in the installation of Boost. See error开发者_运维知识库 below:

checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
dhcp128036164110:cufflinks-1.0.3 jimmy$ ./configure --prefix=/Users/jimmy/Downloads/ --with-boost=/Users/jimmy/Downloads/boost_1_46_1/

If I missed something, could you tell me what is wrong now? Thanks.

PS: I am using Mac OS X (not Windows)

Here is a complete procedure I used for installing Cufflinks from source on a Linux Redhat 64-bit system without root privileges.

Install Boost

1. Create a directory to install into
mkdir ~/bin/boost_1_55_0

2. Download Boost
wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz

3. Unpack Boost
tar xzvf boost_1_55_0.tar.gz

4. Change into boost directory
cd boost_1_55_0

5. Run bootstrap.sh script
./bootstrap.sh

6. Run b2 script
./b2

7. Run b2 script again to install
./b2 install –prefix=/lustre/home/jernest1/bin/boost_1_55_0

8. Add installation directory to several environment variables in ~/.bashrc

Add /lustre/home/jernest1/bin/boost_1_55_0/lib to LD_LIBRARY_PATH
Add /lustre/home/jernest1/boost_1_55_0 to a new variable BOOST_ROOT
Add /lustre/home/jernest1/boost_1_55_0 to a new variable CPLUS_INCLUDE_PATH

9. Source ~/.bashrc
source .bashrc

Install SAM tools

1. Download sam tools
wget http://sourceforge.net/projects/samtools/files/samtools/0.1.17/samtools-0.1.17.tar.bz2

2. Unpack
tar jxvf samtools-0.1.17.tar.bz2

3. Move into the samtools directory
cd samtools-0.1.17

4. Run make
make

5. Make new directories to put sam library files if they don’t already exist
mkdir –p ~/bin/lib
mkdir –p ~/bin/include/bam

6. Copy the libbam.a file to ~/bin/lib/
cp libbam.a ~/bin/lib/

7. Copy header files into ~/bin/include/bam/
cp *.h ~/bin/include/bam/

8. Copy the samtools executable program to a directory in your PATH
cp samtools ~/bin/

9. Add the bam directory to the new variable BAM_ROOT in ~/.bashrc

Install Eigen libraries

1. Download Eigen libraries
wget http://bitbucket.org/eigen/eigen/get/3.2.3.tar.gz

2. Unpack
tar xzvf 3.2.3.tar.gz

3. Move into Eigen directory
cd eigen-eigen-36fd1ba04c12

4. Copy the Eigen subdirectory into ~/bin/include/
cp -r eigen-eigen-36fd1ba04c12/Eigen/ ~/bin/include/

Install Cufflinks

Option 1: Install an official release

1. Make a directory to hold the installation.
mkdir cufflinks_2.2.1

2. Move into that directory cd cufflinks_2.2.1

3. Download cufflinks
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz

4. Unpack
tar xzvf cufflinks-2.2.1.tar.gz

cd cufflinks-2.2.1

5. Run configure script
./configure --prefix=/lustre/home/jernest1/cufflinks_2.2.1 --with-eigen=/lustre/home/jernest1/eigen-eigen-36fd1ba04c12/Eigen --with-bam=/lustre/home/jernest1/bin --with-boost=/lustre/home/jernest1/bin/boost_1_55_0

6. Run make
make

7. Run make install
make install

Optionally, copy ~/cufflinks_2.2.1/bin/cufflinks into ~/bin/

Option 2: install from Github project

1. Make directory to install into
mkdir cufflinks_2014-12-11

2. Move into that directory
cd cufflinks_2014-12-11

2. Download Github project
Click on the "HTTPS clone URL" button to save the URL location to your clipboard

Download
git clone https://github.com/cole-trapnell-lab/cufflinks.git

4. Run autogen.sh to convert configure.ac into configure
./autogen.sh

5. Run configure script
./configure --prefix=/lustre/home/jernest1/cufflinks_2014-12-11 --with-eigen=/lustre/home/jernest1/eigen-eigen-36fd1ba04c12/Eigen --with-bam=/lustre/home/jernest1/bin --with-boost=/lustre/home/jernest1/bin/boost_1_55_0

6. Run make
make

7. Run make install
make install

Optionally, copy ~/cufflinks_2014-12-11/bin/cufflinks into ~/bin/