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Installation and Configuration

Installation Tutorial

1) Update (based on ubuntu 18.04 or 16.04)

sudo apt-get update
sudo apt-get install -y build-essential
sudo apt-get install -y ssh libssl-dev libffi-dev libxml2-dev libxslt1-dev zlib1g-dev zip unzip libfftw3-dev libcurl3 openssl

2) Install python3

sudo apt-get install -y python3 python3-pip python3-dev

3) Install MongoDB, create database paths, and start MongoDB server

cd ~
mkdir -p mongodb
cd mongodb
wget https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz
tar -zxvf mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz


mkdir scdb
mkdir log
sudo ./mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongod --dbpath "./scdb" --port 27017 --wiredTigerCacheSizeGB 1 --fork --logpath "./log/scdb.log"

4) Load database schema & sample data into MongoDB

cd ~/mongodb/
wget http://54.159.6.229/downloads/scDB.zip
unzip scDB.zip
mkdir dumpfiles
mv scDB dumpfiles
mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongorestore dumpfiles

5) Lanuch Single Cell Explorer web application

sudo pip3 install --upgrade pip
sudo pip3 install numpy gunicorn pymongo sklearn pandas django==2.2 torchvision 

cd ~
mkdir singleCell
cd singleCell

wget http://54.159.6.229/downloads/singleCellExplorer.zip
unzip singleCellExplorer.zip
cd singleCellExplorer

python3 manage.py runserver 0.0.0.0:8000