esATAC Installation Tutorial - wzthu/esATAC GitHub Wiki

We recommend to use this package in RStudio with R (version>3.4). Or you have to install pandoc yourself if you use R terminal.

Linux

 We test the esATAC installation under ubuntu 16.0.4.

step1: install the latest R and Rstudio (optional). If you want another version of Rstudio, please check Rstuodio web.

# Download and Install R
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get install r-base r-base-dev

# Download and Install RStudio, the version can be changed
sudo apt-get install gdebi-core
wget https://download1.rstudio.org/rstudio-1.1.419-amd64.deb
sudo gdebi rstudio-1.1.419-amd64.deb
rm rstudio-1.1.419-amd64.deb

Note: If possible, we recommend you install the following packages for ubuntu, because of the need of some R packages.

sudo apt-get install libgsl-dev
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo apt-get install libmysqlclient-dev

step2: install Java.  Here, we prersent the simplest way. For more information, you can see here.

# add the PPA and download Java
sudo add-apt-repository ppa:webupd8team/java
sudo apt update
sudo apt install oracle-java8-installer

# check Java installation and add Java to environment variables
javac -version
sudo apt install oracle-java8-set-default
sudo R CMD javareconf

 Now, you will see "Updating Java configuration in /usr/lib/R" in your command line, that means your Java configuration succeed.

step3: install esATAC.  Open your Rstudio and type the following command.

source("https://bioconductor.org/biocLite.R")
biocLite("esATAC")

 Now, you can have a nap and wait for the accomplishment of installation.

Windows

 We test the esATAC installation under Win10 education version 1703.

step1: install the latest R , Rstudio (optional) and Rtools.
 Download R, Rstudio and Rtools. All these files are .exe file and can be installed easily on windows.

Note: If possible, please install R and Rtools in the default pathway, we found that the customized pathway would cause error when using Rtools to compile C/C++ code. Remeber to add Rtools to environment variables (you can choose this option during the installation).

step2: install Java and add Java to environment variables. Download Java SE and install it.

step3: install esATAC.  Open your Rstudio and type the following command.

source("https://bioconductor.org/biocLite.R")
biocLite("esATAC")

 Now, wait for the accomplishment of installation.
Note:If you encounter error during installing esATAC, please reinstall the error package.

MAC OS

 We test the esATAC installation under macOS Sierra 10.12.6.

step1: install the latest R , Rstudio (optional).

 Download R (R-3.4.*.pkg), Rstudio (RStudio.*.dmg). They can be installed easily on macOS .

step2: install Java

Download Java SE and install it.

If the java virtue machine dynamic library does not exist in /usr/local/lib, you may try to create link like this:

sudo ln -f -s $(/usr/libexec/java_home)/lib/server/libjvm.dylib /usr/local/lib

The path of libjvm.dylib may need to be revised according to your own machine.

step3: install esATAC.  Open your Rstudio and type the following command.

source("https://bioconductor.org/biocLite.R")
biocLite("esATAC")

 Now, wait for the accomplishment of installation.
Note:If you encounter error during installing esATAC, please reinstall the error package.