lev-kuznetsov/mev

MultiExperiment Viewer

#MultiExperiment Viewer

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The new web client MeV

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To build you need to have Java 7, maven 3.0+, R 3.0+, node 4.5.0 and npm 2.15+ The following instructions pertain to Ubuntu 16.04, OSX install procedure will slightly differ

##Development ###Get Source Fork the repository then download source

mkdir -p ~/git/mev
cd ~/git/mev
git clone https://github.com/yourusername/mev.git
git remote add upstream https://github.com/dfci-cccb/mev.git 

###Install Dependencies ####ProtoBuff

sudo apt-get install build-essential libtool
sudo apt-get install autoconf
cd ~/git
git clone https://github.com/dfci-cccb/protobuf.git
cd protobuf
./autogen.sh
./configure --prefix=/usr
make
make check
sudo make install

#####Install R Dependencies

sudo apt-get install gfortran
sudo apt-get install libreadline-dev

Install R from http://lib.stat.cmu.edu/R/CRAN/

######Install R Packages Install from R console #######Multtest

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

#######DESeq Dependenciessudo apt install libxml2-dev

source("http://bioconductor.org/biocLite.R");
biocLite("DESeq");

######RProtoBuff Dependencies: sudo apt install libcurl4-gnutls-dev

###Build Web App

cd ~/git/mev
mvn clean install

###Web Client Assumes node 4.5.0 and npm version 2.15+ is installed is intalled ####Install Node Packages Dependency: (Required: Required by Vegajs for mevNetworkGraph)

sudo apt-get install libcairo2-dev libjpeg-dev libgif-dev

npm install -g linklocal
npm install -g bower
npm install -g gulp grunt

####Build Web Client

cd ~/git/mev/web/src/main/javascript/edu/dfci/cccb/mev/web/ui
linklocal -r
bower install
npm run dev
gulp

###Run After installing the dependencies and building web app and web client you're ready to run. First launch RServe, then the WebApp ####Start RServe

cd ~/git/mev/web
mvn rserve:run

Note: when running for the first time the above command will install required R packages

####Start Web Server

cd ~/git/mev/web
mvn jetty:run

You may now point your browser to http://localhost:8080