https://github.com/intermine/intermine-steps
InterMine 2.0 Prototype preserving history of Steps
https://github.com/intermine/intermine-steps
Last synced: 6 months ago
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InterMine 2.0 Prototype preserving history of Steps
- Host: GitHub
- URL: https://github.com/intermine/intermine-steps
- Owner: intermine
- Created: 2013-01-15T16:00:58.000Z (almost 13 years ago)
- Default Branch: master
- Last Pushed: 2014-02-12T17:50:06.000Z (almost 12 years ago)
- Last Synced: 2025-03-13T02:16:08.936Z (10 months ago)
- Language: JavaScript
- Homepage:
- Size: 5.5 MB
- Stars: 2
- Watchers: 3
- Forks: 2
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
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README
# InterMine Steps
InterMine 2.0 Prototype preserving history of Steps
**[Questions & Answers](docs/q-n-a.md)**
##Install
###Required Packages###
####NPM
Make sure you have [node.js](https://github.com/joyent/node/wiki/Installing-Node.js-via-package-manager) installed which installs its package manager, [npm](https://npmjs.org/), 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](http://davidwalsh.name/upgrade-nodejs))
```bash
$ sudo npm cache clean -f
$ sudo npm install -g n
$ sudo n stable
```
Alternatively, install `node.js` [from sources](https://github.com/joyent/node/wiki/Installing-Node.js-via-package-manager#debian-lmde).
####Bower (optional)
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](http://bower.io/):
```bash
$ sudo npm install -g bower
$ bower 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.
####Grunt (optional)
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](http://gruntjs.com/) that builds Steps and munges the different tools and its deps into single builds. To [install Grunt](http://gruntjs.com/getting-started) and make a build:
```bash
$ sudo npm install -g grunt-cli
$ grunt
```
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:
```bash
$ watch --color grunt
```
###Steps###
Clone this repository
`
git clone git@github.com:intermine/intermine-steps.git my-steps-directory
`
and install the app dependencies:
```bash
$ cd my-steps-directory
$ npm install
```
##Startup
Now we can startup Steps on a custom port and visit it in the browser.
From your steps directory
```bash
$ PORT=4444 coffee server/server.coffee
```
If you need to get CoffeeScript `coffee` command, do the following step:
```bash
$ sudo npm install coffee-script -g
```
If you need to install the module `flatiron`
```bash
$ sudo npm install flatiron -g
```
##Configuration
The default tools configuration is in `tools/config.coffee`.
#### Registry of tools labels ####
You will also find a registry of tool labels that will show up in various scenarios.
For example:
```coffeescript
{
'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.