gu-mi · December 14, 2015 07:59 · Feb 28, 2013 · Feb 28, 2013 · Feb 28, 2013 · Feb 28, 2013
diff --git a/installation of Cufflinks b/installation of Cufflinks
@@ -14,17 +14,7 @@ Installing Boost C++ libraries
   # Build:
   ./b2
   # Install:
-  ./b2 install
-
-The Boost C++ Libraries were successfully built!
-
-The following directory should be added to compiler include paths:
-
-    /Users/mig/Downloads/boost_1_53_0
-
-The following directory should be added to linker library paths:
-
-    /Users/mig/Downloads/boost_1_53_0/stage/lib
+  sudo ./b2 install
 
 Installing Samtools
 1. Downlaod samtools at http://sourceforge.net/projects/samtools/files/

diff --git a/installation of Cufflinks b/installation of Cufflinks
@@ -16,6 +16,16 @@ Installing Boost C++ libraries
   # Install:
   ./b2 install
 
+The Boost C++ Libraries were successfully built!
+
+The following directory should be added to compiler include paths:
+
+    /Users/mig/Downloads/boost_1_53_0
+
+The following directory should be added to linker library paths:
+
+    /Users/mig/Downloads/boost_1_53_0/stage/lib
+
 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.

diff --git a/installation of Cufflinks b/installation of Cufflinks
@@ -1,7 +1,7 @@
 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
+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/

diff --git a/installation of Cufflinks b/installation of Cufflinks
@@ -0,0 +1,130 @@
+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
+
+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:
+  ./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