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Patch install INSTALL #2

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ec088e1
Better Rmath spec
mmterpstra Oct 25, 2017
2ce46d1
Clarity update install
mmterpstra Oct 25, 2017
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41 changes: 18 additions & 23 deletions INSTALL
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Expand Up @@ -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 #
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