Instructions for installing Cufflinks and related tools in Mac OS X

installation of Cufflinks

Follow the steps at http://cufflinks.cbcb.umd.edu/tutorial.html

1. Download Cufflinks version 2.0.2 (BETA), Source code
2. tar -zxvf cufflinks-2.0.2.tar.gz (before final installation, make sure related tools are installed! See below)

Installing Boost C++ libraries
1. Download Boost at http://www.boost.org/users/download/
2. The bjam boost engine is also required. If MacPort is installed, then use the command sudo port install boost. It will take care of everything.
3. If #2 won't work, try (preferred way!)
  tar -xzf boost_1_50_0.tar.gz
  cd boost_1_50_0
  # Configure (and build bjam):
  ./bootstrap.sh --prefix=/some/dir/you/would/like/to/prefix
  # Build:
  ./b2
  # Install:
  sudo ./b2 install

Installing Samtools
1. Downlaod samtools at http://sourceforge.net/projects/samtools/files/
2. tar zxvf samtools-0.1.18.tar.bz2 and cd to the SAM tools source directory.
3. Build the SAM tools by typing make at the command line.
4. Copy libbam.a to the lib/ directory (e.g. /usr/local/lib/)
5. Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
6. sudo cp -a ./samtools-0.1.18/*.h /usr/local/include/bam (copy headers (files ending in .h) to the include/bam directory)
7. sudo cp -a ./samtools-0.1.18 /usr/local

Installing the Eigen libraries
1. Download Eigen at http://eigen.tuxfamily.org/
2. tar zxvf eigen-eigen-5097c01bcdc4.tar.bz2
3. sudo cp -a ./Eigen /urs/local/include

...Now, finally we can build Cufflinks
1. cd cufflinks-2.0.2
2. ./configure

In the terminal, we will see...

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) awk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... darwin
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 >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-apple-darwin12.2.0
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-mt... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-apple-darwin12.2.0
checking for struct sysinfo.totalram... no
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... yes
checking whether HW_PHYSMEM is declared... yes
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands

-- cufflinks 2.0.2 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -arch x86_64 -O3  -DNDEBUG  -pthread -I/opt/local/include -I/usr/local/include
  GCC version:         i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
  Host System type:    i686-apple-darwin12.2.0
  Install prefix:      /usr/local
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <[email protected]> with questions and bug reports.

Finally, make and install Cufflinks.
make
make install