diff --git a/INSTALL b/INSTALL index 96c707e..e89bd8e 100644 --- a/INSTALL +++ b/INSTALL @@ -40,38 +40,33 @@ If it doesn't run, i'm afraid you've got to compile the code (See section B). # B. COMPILE FASTQTL ON LINUX # ############################################################################################ -(B.1) INSTALL MATH R LIBRARY - (1) Download R source code: wget http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz - (2) Unzip R source code: tar xzvf R-3.2.0.tar.gz - (3) Go to R source code folder: cd R-3.2.0 - (4) Configure Makefile: ./configure - (5) Go to R math library folder: cd src/nmath/standalone - (6) Compile the code: make - (7) Go 2 folder backward: cd ../.. - (8) Save the current path: RMATH=$(pwd) - +(B.1) INSTALL R development version + (1) Install Rmath header files + On Debian/Ubunutu, just run: `sudo apt-get install r-base-dev` + (2) Find the Rmath.h file `find /usr/ -iname Rmath.h` + (B.2.1) INSTALL BOOST (if not already installer, OPTION1: MANUALLY) - (1) Download BOOST: http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.gz/download - (2) Unzip the package: tar xzvf boost_1_58_0.tar.gz - (3) Go in the folder: cd boost_1_58_0 - (4) Install required packages: ./bootstrap.sh --prefix=/home/olivier/Desktop/myInstall --with-libraries=iostreams,program_options + (1) Download BOOST: `http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.gz/download` + (2) Unzip the package: `tar xzvf boost_1_58_0.tar.gz` + (3) Go in the folder: `cd boost_1_58_0` + (4) Install required packages: `./bootstrap.sh --prefix=/home/olivier/Desktop/myInstall --with-libraries=iostreams,program_options` (B.2.2) INSTALL BOOST (if not already installer, OPTION2: AUTOMATICALLY) Many Linux distribution have BOOST package already built. - On Debian/Ubunutu, just run: sudo apt-get install libboost-dev - On Redhat/CentOS, just run: yum install boost-devel + On Debian/Ubunutu, just run: `sudo apt-get install libboost-dev` + On Redhat/CentOS, just run: `yum install boost-devel` -(B.3) INSTALL GSL (if not already installed) +(B.3) INSTALL GSL 1.16 (if not already installed) Most Linux distribution have GSL package already built. - On Debian/Ubunutu, just run: sudo apt-get install libgsl0-dev - On Redhat/CentOS, just run: yum install gsl-devel + On Debian/Ubunutu, just run: `sudo apt-get install libgsl0-dev` + On Redhat/CentOS, just run: `yum install gsl-devel` (B.4) COMPILE FASTQTL - (1) Go to the fastqtl folder: cd FastQTL-2.165 - (2) Compile the code running: make cleanall && make - This later step needs the RMATH variable in A.1.8 to be defined. - This can be specified here by: make RMATH=/my/path/to/r/src + (1) Go to the fastqtl folder: `cd FastQTL-2.165` + (2) Compile the code running: `make cleanall && make` + This later step needs the Rmath library see (B.1) from R and the `obj\` subfolder to be present. + This can be specified here by: `mkdir obj && make RMATH=/usr/share/R/ LIB_MATH='-lRmath -I/usr/share/R/include/Rmath.h'` ############################################################################################ # C. RUN FASTQTL ON MACOS #