INSTALLING BOOST LIBRARIES, TOPHAT, SAM TOOLS, CUFFLINKS ON CENTOS7

Boost Libraries

$ tar zxvfp boost_1_62_0.tar.gz

$ cd boost_1_62_0/

$ ./bootstrap.sh --prefix=/BiO/hadoop/program/linux_tools/boost_1_62_0 --with-libraries=all

$ ./b2

$ ./b2 install

$ export BOOST_ROOT=/BiO/hadoop/program/linux_tools/boost_1_62_0

$ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH

TopHat

$ tar xzvf tophat-2.1.1.tar.gz

$ cd tophat-2.1.1

$ ./configure --prefix /BiO/hadoop/program/linux_tools/tophat-2.1.1 \
 --with-boost=/BiO/hadoop/program/linux_tools/boost_1_62_0

$ make

$ sudo make install

SAM tools

$ cd samtools-0.1.19/ 

$ make

$ mkdir -p /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/bin  \
/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/include/bam \
/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/lib \

$ cp libbam.a /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/lib/

$ cp *.h /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/include/bam/

Cufflinks

$ tar jxfp 3.2.8.tar.bz2

$ cd eigen-eigen-07105f7124f9/

$ mkdir /BiO/hadoop/program/linux_tools/isbyeon_test/eigen3

$ cp -rv ./Eigen/ /BiO/hadoop/program/linux_tools/isbyeon_test/eigen3

$ export EIGEN_CPPFLAGS="-I/BiO/hadoop/program/linux_tools/isbyeon_test/eigen3"

$ tar zxvfp cufflinks-2.2.1.tar.gz

$ cd cufflinks-2.2.1/

$ ./configure --prefix=//BiO/hadoop/program/linux_tools/isbyeon_test/cufflinks-2.2.1 \
--with-boost=/BiO/hadoop/program/linux_tools/boost_1_62_0 \
--with-bam=/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19

$ make

$ make install