Demo Web Application
To install pagoda2 please follow the instructions below.
Install system dependencies, example here provided for Ubuntu
sudo apt-get update sudo apt-get -y install build-essential cmake gsl-bin libgsl0-dev libeigen3-dev libboost-all-dev libssl-dev libcurl4-openssl-dev libssl-dev libcairo2-dev libxt-dev libgtk2.0-dev libcairo2-dev xvfb xauth xfonts-base
You need R >=3.4.0 to install this package on a mac. For installation please refer to cran
You need the homebrew package manager
Run these commands in a terminal:
brew update brew install cmake boost eigen gsl curl openssl wget
To enable R to use the parallelized functions in the C++ code, you need another version of the clang++-Compiler for mac.
This is compatible with OS X >= 10.11
Follow these instructions to install clang4 with openmp support:
- Download the clang4-r.pkg (263.6 mb) from https://uofi.box.com/v/r-macos-clang-pkg
- Install it!
Here is a more in depth explanation what is going on and a script to do what the GUI-Installer does by yourself. For Pagoda2 you only need the clang part, not the gfortran part. openmp in r on OS X
Install X windows system for mac
Go to https://www.xquartz.org/ and follow the instructions for installing the package.
Install gfortran for Mac
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
Install pagoda2 package
# Install Bioconductor dependencies source("http://bioconductor.org/biocLite.R") biocLite(c("GO.db", "org.Hs.eg.db","org.Mm.eg.db", "pcaMethods"), suppressUpdates=TRUE) library(devtools) install_github("igraph/rigraph") # Don't install with install.packages() install_github("jkrijthe/Rtsne",ref="openmp") install.packages(c("Cairo","urltools")) # Install pagoda install_github("hms-dbmi/pagoda2") library('pagoda2') # Pagoda2 is now ready to use
Alternative Install padoga2 as a docker container
Please note that the docker container is as of March 2018 not up to date with the main project branch and all the latest features are missing. It is strongly recommended that you install the main release.