How to rectify issues occurring while installing Cufflinks and Boost? - macos

Question

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 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)

Answer 1

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/