SGDAllianceData

Setup (Required)

• Install Node if you don't have it installed already

• Currently using node v10.12.0 for development

• Make sure you're running the scripts in a virtual environment

• Makefile has all the commands you need to run the scripts to produce the data files.

• To install required packages run the this command:

• $ is no part of the command(s), just visual cue since terminal looks like that.

Node Version Management installation (optional)

• If you do not have nvm installed, please follow the following to setup node environment on your machine. This is for Mac OS.
• NVM allows you to work with different versions of node in case you have different project with varying node versions.

NVM with Homebrew

$ brew update
$ brew install nvm
$ mkdir ~/.nvm
$ vim ~/.bash_profile

bash_profile nvm setup

• Add the following lines to your bash_profile

$ export NVM_DIR=~/.nvm
$ source $(brew --prefix nvm)/nvm.sh

• Go back to your terminal after adding above lines to your bash_profile
• Run the following commands to activate reload bash_profile since you just made a change to it.

$ source ~/.bash_profile

installing node with nvm

• You can install any node version you want
• Check the list of node releases
• For this project we used node 10.12.0, so go ahead and install that with nvm. See below.

$ nvm install 10.12.0

• To see list of node version available in your machine run the following

$ nvm ls

• To pick specific node version to use for your project run the following.

$ nvm use 10.12.0

• To set default node version in case you don't wanna be picking node version each time you're working on node related tasks. Do this outside your virtual environment

$ nvm alias default 10.12.0

Run everything in single command

$ Make build

• No need to run commands below if you run this as it includes all the commands

Running Commands one by one

$ Make setup

File dependencies (Required if running Makefile commands one by one)

• Some of the scripts depend on pather_search_results.txt and disease_association.txt files to produce output json files
• Run the following to build the depencies before running the scripts

$ Make build-disease
$ Make build-panther

Disease Association file

$ Make run-disease

Phenotype File

$ Make run-phenotype 

Expression File

$ Make run-expression 

Basic Gene Information File

$ Make run-bgi

File structure

• This is where the modules that get necessary data are

|-- src
|   |-- basic_gene_information
|   |   |-- basic_gene_information.py
|   |-- data_assets
|   |   |-- disease_association.txt
|   |   |-- panther_search_results.txt
|   |-- data_dump
|   |   |-- json data files are deposited here
|   |-- data_helpers
|   |   |-- data_helpers.py
|   |-- disease
|   |   |-- disease.py 
|   |-- expression
|   |   |-- expression.py
|   |-- phenotype
|   |   |-- phenotype.py  
|   |-- models
|   |   |-- models.py