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Getting Started

To start with the Clinical Meteor Software Development Kit, we're going to need to set up a complete development environment. There's a large ecosystem of tools to use, so the focus in this document is on tools that are known to work together well on Mac OSX and are popular within the Meteor community.

App Development
Meteor - Isomorphic javascript/node environment.
GitHub Desktop App - For synchronizing and managing code.
Visual Studio Code - Editor with support for large files (genomics, big data) and good javascript refactoring tools.

Platform Development
Java 8 - Needed QA testing tools.
Node JS - Server-side javascript environment. Use the LTS release.
Visual Studio - Community 2017 - C++ compilers needed for some Node libraries.

Chrome Environment

Clinical Meteor prefers a Chrome environment. So much so, that its arguably an alternative Chrome OS. Not only will we be targeting Chrome as our preferred browser; we'll also be installing utilities as Chrome extensions; using a code editor built on Chrome, and using Chrome in our QA test runner. Clinical Meteor supports other browsers (particularly Firefox and Safari), but the bulk of it's work is done with Chrome.

Once you get Chrome installed, we recommend the following extensions; which will help develop Clinical Meteor apps.

Chrome - Prefered web browser.
Postman HTTP/REST Utility - HTTP protocol utility for programming REST interfaces.
MeteorDevTools - Blaze, DDP, and Minimongo debugging utilities.

Version Control Software

The easiest way to install git is to install the GitHub Desktop App. You'll then have access to both the GUI and the command line.

$ git config --global user.name "Jane Doe"
$ git config --global user.email janedoe@example.com
$ git config --global core.editor atom -w

Meteor Installation Walkthrough

This quickstart is written for Mac OSX Mavericks, and is a bit more verbose than other installation instructions. It should hopefully cover a few edge cases, such as setting your path, which can cause an installation to go awry.

# install meteor
npm install -g meteor. 

# check it's installed correctly
meteor --version

# install npm
curl -0 -L https://npmjs.org/install.sh | sh

# check node is installed correctly
node --version

# check npm is installed correctly
npm -version

# find your npm path
which npm

# make sure npm is in your path
sudo nano ~/.profile
  export PATH=$PATH:/usr/local/bin

If you have any problems with EACCESS pr ENOENT errors, check the file permissions of your NPM directories.
https://docs.npmjs.com/getting-started/fixing-npm-permissions

Database Tools

Robomongo - A sweet, sweet database management tool for MongoDB.

Here's the script the author uses when setting up a new development workstation. It's certainly not the only environment setup script, and it's by no means authoritative. It's simply what seems to work.

# install stand-alone mongo with the gui installer
http://www.mongodb.org/dr//fastdl.mongodb.org/osx/mongodb-osx-x86_64-2.6.3.tgz/download

# or install from command line
curl http://downloads.mongodb.org/osx/mongodb-osx-x86_64-2.6.3.tgz > mongodb-osx-x86_64-2.6.3.tgz
tar -zxvf mongodb-osx-x86_64-2.6.3.tgz
mkdir -p /var/mongodb
cp -R -n mongodb-osx-x86_64-2.6.3/* /usr/local/mongodb

# make sure mongo is in your local path
nano ~/.profile
  export PATH=$PATH:/usr/local/mongodb/bin

# or install it to the global path
nano /etc/paths
  /usr/local/mongodb/bin

# create mongo database directory
mkdir /data/
mkdir /data/db
chown -R username:admin /data

# run mongodb server
mongod
ctrl-c

# check that you can connect to your meteor app with stand-alone mongo
terminal-a$ meteor create helloworld
terminal-a$ cd helloworld
terminal-a$ meteor

terminal-b$ mongo -port 3001

# install robomongo database admin tool
http://robomongo.org/

# check you can connect to your mongo instance with robomongo
terminal-a$ meteor create helloworld
terminal-a$ cd helloworld
terminal-a$ meteor

Dock$ Robomongo > Create > localhost:3001

# install node-inspector
terminal-a$  npm install -g node-inspector

# start meteor
terminal-a$  cd helloworld
terminal-a$  NODE_OPTIONS='--debug-brk --debug' mrt run

# alternatively, some people report this syntax being better
terminal-a$  sudo NODE_OPTIONS='--debug' ROOT_URL=http://helloworld.com meteor --port 80

# launch node-inspector along side your running app
terminal-b$  node-inspector

# go to the URL given by node-inspector and check it's running
http://localhost:8080/debug?port=5858

# install jshint
npm install -g jshint

# run code analysis on local directory
cd helloworld
jshint .

Project Management Tools

Popular project management tools.

Slack - Collaborative project tracking feeds.
InVision Sync - Collaborative wireframing and prototyping.
Zenhub.io - Project management Kanban boards for GitHub.
LucidChart - Flowcharting software.