This document describes how to install/compile FastQTL on both Linux & Mac OS
A. RUN FASTQTL ON LINUX
B. COMPILE FASTQTL ON LINUX
C. RUN FASTQTL ON MAC OS
D. COMPILE FASTQTL ON MAC OS
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# A. RUN FASTQTL ON LINUX #
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Just run: ./bin/fastqtl.static --help
If it works, you should get this screen output:
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Fast QTL
* Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
* Contact : olivier.delaneau@gmail.com
* Webpage : http://fastqtl.sourceforge.net/
* Version : v2.0
Basic options:
--help Produces this help
--silent Silent mode on terminal
--seed arg (=1434116729) Random number seed. Useful to replicate
...
Parallelization:
-K [ --chunk ] arg Specify which chunk needs to be
processed
--commands arg Generates all commands
-R [ --region ] arg Region of interest.
-------------------------------
If it doesn't run, i'm afraid you've got to compile the code (See section B).
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# B. COMPILE FASTQTL ON LINUX #
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(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=$(pwd)
(B.2.1) INSTALL BOOST (if not already installer, OPTION1: MANUALLY)
(1) Download BOOST: http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.gz/download
(2) Unzip the package: tar xzvf boost_1_58_0.tar.gz
(3) Go in the folder: cd boost_1_58_0
(4) Install required packages: ./bootstrap.sh --prefix=/home/olivier/Desktop/myInstall --with-libraries=iostreams,program_options
(B.2.2) INSTALL BOOST (if not already installer, OPTION2: AUTOMATICALLY)
Many Linux distribution have BOOST package already built.
On Debian/Ubunutu, just run: sudo apt-get install libboost-dev
On Redhat/CentOS, just run: yum install boost-devel
(B.3) INSTALL GSL (if not already installed)
Most Linux distribution have GSL package already built.
On Debian/Ubunutu, just run: sudo apt-get install libgsl0-dev
On Redhat/CentOS, just run: yum install gsl-devel
(B.4) COMPILE FASTQTL
(1) Go to the fastqtl folder: cd FastQTL-2.165
(2) Compile the code running: make cleanall && make
This later step needs the RMATH variable in A.1.8 to be defined.
This can be specified here by: make RMATH=/my/path/to/r/src
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# C. RUN FASTQTL ON MACOS #
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(C.1) INSTALL HOMEBREW (if not already installed)
(1) Run: ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
(C.2) INSTALL BOOST (if not already installed)
(1) Run: brew install boost
(C.3) INSTALL GSL (if not already installed)
(1) Run: brew install gsl
(C.4) TEST FASTQTL:
(1) Run: ./bin/fastqtl.macos --help
If it works, you should get this screen output:
-------------------------------
Fast QTL
* Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
* Contact : olivier.delaneau@gmail.com
* Webpage : http://fastqtl.sourceforge.net/
* Version : v2.0
Basic options:
--help Produces this help
--silent Silent mode on terminal
--seed arg (=1434116729) Random number seed. Useful to replicate
...
Parallelization:
-K [ --chunk ] arg Specify which chunk needs to be
processed
--commands arg Generates all commands
-R [ --region ] arg Region of interest.
-------------------------------
If it doesn't run, i'm afraid you've got to compile the code (See section D).
############################################################################################
# D. COMPILE FASTQTL ON MACOS #
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(D.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=$(pwd)
(D.2) INSTALL HOMEBREW (if not already installed)
(1) Run: ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
(D.3) INSTALL BOOST (if not already installed)
(1) Run: brew install boost
(D.4) INSTALL GSL (if not already installed)
(1) Run: brew install gsl
(D.5) COMPILE FASTQTL
(1) Go to the fastqtl folder: cd FastQTL-2.165
(2) Compile the code running: make cleanall && make macos
This later step needs the RMATH variable in D.1.8 to be defined.
This can be specified here by: make RMATH=/my/path/to/r/src