Name: intermine-steps
Owner: InterMine
Description: InterMine 2.0 Prototype preserving history of Steps
Created: 2013-01-15 16:00:58.0
Updated: 2017-01-20 16:53:34.0
Pushed: 2014-02-12 17:50:06.0
Size: 5772
Language: JavaScript
GitHub Committers
| User | Most Recent Commit | # Commits |
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InterMine 2.0 Prototype preserving history of Steps
Make sure you have node.js installed which installs its package manager, npm, too.
node.js version v0.6.19, currently supported on Ubuntu, is too old for npm to work. You have two options:
You can upgrade to the last release using npm itself (see this page)
do npm cache clean -f
do npm install -g n
do n stable
Alternatively, install node.js from sources.
You can skip this step if you just want to start an instance of Steps without making changes to it.
The app fetches a bunch of tools and their vendor dependencies, do so by using Bower:
do npm install -g bower
wer install
It fetches libraries defined in the bower.json file. So, whenever you make changes to this file, you need to re-run the bower install command and the grunt command which we will discuss next.
You can skip this step if you just want to start an instance of Steps without making changes to it.
Another tool we are using is Grunt that builds Steps and munges the different tools and its deps into single builds. To install Grunt and make a build:
do npm install -g grunt-cli
unt
The build steps are defined in the file Gruntfile.coffee. Whever you make changes to this file, or whenever you make changes to the /src or /tools directory, you need to run a new build using the grunt command.
When you are developing, it is recommended that you watch the default Grunt task like so:
tch --color grunt
Clone this repository
git clone git@github.com:intermine/intermine-steps.git my-steps-directory
and install the app dependencies:
my-steps-directory
m install
Now we can startup Steps on a custom port and visit it in the browser.
From your steps directory
RT=4444 coffee server/server.coffee
If you need to get CoffeeScript coffee command, do the following step:
do npm install coffee-script -g
If you need to install the module flatiron
do npm install flatiron -g
The default tools configuration is in tools/config.coffee.
You will also find a registry of tool labels that will show up in various scenarios.
For example:
'label': 'mRNA subcellular localisation (fly-FISH)'
'weight': 10
'context': [ 'have:list', 'type:Gene' ]
'place': 'right'
'category': [ 'Category 1' ]
'extra': [ 'chart', 'flyfish' ]
with
| label | This is the label that will show up in a menu. All the text from this label is searchable. |
|---|---|
| weight | Will determine the order in which labels will show. Higher number means higher position. Labels below 10 do not initially show in a menuand one needs to click a button to expand the menu and show these. |
| context | This label will show up when all of the context rules are met. The rules are just messages triggered by currently running tools. |
| place | In which menu is this label to appear? |
| category | An array allowing you to create a nested structure where your label will appear. |
| extra | Parameters passed to a tool to differentiate between variants of it. |