1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
|
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
############################################################################################
# A. RUN FASTQTL ON LINUX #
############################################################################################
Just run: ./bin/fastqtl.static --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 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=$(pwd)
(B.2.1) INSTALL BOOST (if not already installer, OPTION1: MANUALLY)
(1) Download BOOST: http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.gz/download
(2) Unzip the package: tar xzvf boost_1_58_0.tar.gz
(3) Go in the folder: cd boost_1_58_0
(4) Install required packages: ./bootstrap.sh --prefix=/home/olivier/Desktop/myInstall --with-libraries=iostreams,program_options
(B.2.2) INSTALL BOOST (if not already installer, OPTION2: AUTOMATICALLY)
Many Linux distribution have BOOST package already built.
On Debian/Ubunutu, just run: sudo apt-get install libboost-dev
On Redhat/CentOS, just run: yum install boost-devel
(B.3) INSTALL GSL (if not already installed)
Most Linux distribution have GSL package already built.
On Debian/Ubunutu, just run: sudo apt-get install libgsl0-dev
On Redhat/CentOS, just run: yum install gsl-devel
(B.4) COMPILE FASTQTL
(1) Go to the fastqtl folder: cd FastQTL-2.165
(2) Compile the code running: make cleanall && make
This later step needs the RMATH variable in A.1.8 to be defined.
This can be specified here by: make RMATH=/my/path/to/r/src
############################################################################################
# C. RUN FASTQTL ON MACOS #
############################################################################################
(C.1) INSTALL HOMEBREW (if not already installed)
(1) Run: ruby -e "$(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 #
############################################################################################
(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
|
