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+#=======================================# |
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+### INSTALLATION INSTRUCTIONS FOR MAC ### |
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+#=======================================# |
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+ |
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+#######Begin by installing xcode and xcode command line tools####### |
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+ |
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+##Install Xcode using the appstore (free) |
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+ |
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+##Open a terminal and instal Xcode command line tools |
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+xcode-select --install |
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+ |
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+##Agree to Xcode license in Terminal |
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+sudo xcodebuild -license |
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+ |
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+ |
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+ |
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+#######The following steps may be necessary in order to install some of chromstaR dependencies####### |
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+ |
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+##In a terminal window, check if libcurl, libxml and ccache are installed |
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+curl-config --version |
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+xmllint --version |
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+ccache --version |
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+ |
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+##if not installed, install (or update) them through macports |
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+##Install macports from this website https://www.macports.org/install.php |
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+##Go back to terminal and selfupdate macports |
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+sudo port -v selfupdate |
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+##install libcurl, libxml and ccache |
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+sudo port install curl libxml libxml2 ccache |
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+ |
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+ |
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+##Install the gfortran libraries |
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+curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 |
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+sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C / |
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+ |
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+ |
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+ |
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+#######As of June 5th, 2015, the following steps are needed to install chromstaR on OS X Yosemite (10.10) and below####### |
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+ |
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+##Install Xcode using the appstore (free) |
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+ |
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+##Open a terminal and instal Xcode command line tools |
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+xcode-select --install |
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+ |
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+##Agree to Xcode license in Terminal |
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+sudo xcodebuild -license |
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+ |
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+##OSX doesn't use the latest version of the GCC compiler allowing to use multithreading in R. To make the installation of chromstaR |
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+##successful, a recent version of GCC needs to be installed. This can be done using Homebrew |
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+##Note: you may have to chown the following directories in order for homebrew to install the previous packages and library |
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+sudo chown {your-user-name} /usr/local/bin
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+sudo chown {your-user-name} /usr/local/include
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+sudo chown {your-user-name} /usr/local/lib
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+sudo chown {your-user-name} /usr/local/share
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+ |
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+##Install homebrew and the lastest versions of GCC (very long, takes 30 mins to 2 hours to compile) and CCache |
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+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" |
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+brew install gcc --without-multilib |
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+brew install clang-omp |
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+brew install ccache |
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+##Note: be careful in warning messages provided by homebrew and follow it's instruction/suggestions |
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+ |
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+ |
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+#Modify ~/.R/Makvars in order to tell R which compiler to use. Replace everything in that file by what is below |
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+########################################################### |
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+CFLAGS += -O3 -Wall -pipe -pedantic -std=gnu99 |
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+CXXFLAGS += -O3 -Wall -pipe -Wno-unused -pedantic |
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+ |
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+CC=ccache gcc |
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+CXX=ccache g++ |
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+SHLIB_CXXLD=g++ |
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+ |
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+SHLIB_OPENMP_CFLAGS = -fopenmp |
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+SHLIB_OPENMP_CXXFLAGS = -fopenmp |
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+SHLIB_OPENMP_FCFLAGS = -fopenmp |
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+SHLIB_OPENMP_FFLAGS = -fopenmp |
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+ |
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+ |
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+FC=ccache gfortran |
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+F77=ccache gfortran |
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+MAKE=make -j8 |
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+ |
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+########################################################### |
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+ |
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+ |
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+##Download chromstaR packages locally, as you may have to modify some of the files |
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+##In chromstaR Package, modifies /scr/R_interface.cpp and src/scalehmm.h |
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+##to replace #include <omp.h> by #include <libiomp/omp.h> |
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+##if these corrections were already present in the files, please ignore and install directly from bitbucket (see below) |
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+ |
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+ |
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+#=====================================================# |
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+### INSTALLATION INSTRUCTIONS FOR LINUX AND WINDOWS ### |
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+#=====================================================# |
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+ |
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+##In R, install the following packages |
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install.packages('devtools')
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source("http://bioconductor.org/biocLite.R")
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biocLite("GenomicRanges")
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biocLite("GenomicAlignments")
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biocLite("BSgenome")
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library(devtools) |
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+##If you have modified R_interface.cpp and scalhmm.h in chromstaR |
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+install.packages("path-to-chromstaR-package", type='source', repos=NULL)
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+##If you have not modified chromstaR |
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install_bitbucket('chakalakka/chromstaR', username='chakalakka', password='chromstaR2015')
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install_github('chakalakka/chromstaRExampleData')
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+ |
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+ |
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+ |
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+ |
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@@ -1,9 +1,14 @@ |
| 1 | 1 |
#include "utility.h" |
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#include "scalehmm.h" |
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#include <vector> // storing density functions in multivariate |
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-#include <omp.h> // parallelization options |
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#include <string> // strcmp |
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+#if defined TARGET_OS_MAC || defined __APPLE__ |
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+#include <libiomp/omp.h> // parallelization options on mac |
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+#elif defined __linux__ || defined _WIN32 || defined _WIN64 |
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+#include <omp.h> // parallelization options |
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+#endif |
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+ |
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static ScaleHMM* hmm; // declare as static outside the function because we only need one and this enables memory-cleanup on R_CheckUserInterrupt() |
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static int** multiO; |
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| 1 | 1 |
#ifndef SCALEHMM_H |
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#define SCALEHMM_H |
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-#include <omp.h> // #pragma omp parallel |
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#include <R.h> // R_CheckUserInterrupt() |
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#include <vector> // storing density functions |
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#include <time.h> // time(), difftime() |
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@@ -9,6 +8,12 @@ |
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#include "densities.h" |
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#include <string> // strcmp |
| 11 | 10 |
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+#if defined TARGET_OS_MAC || defined __APPLE__ |
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+#include <libiomp/omp.h> // parallelization options on mac |
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+#elif defined __linux__ || defined _WIN32 || defined _WIN64 |
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+#include <omp.h> // parallelization options |
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+#endif |
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+ |
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class ScaleHMM {
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public: |
