biojs2galaxy

biojs2galaxy
============


A fast tool to convert BioJS components into Galaxy visualization plugins.

__Warning__: This tool is in a __ALPHA__ stage. Use at your own risk.

It was tested so far with the

* msa component.
* sequence

How to add a (BioJS) Plugin
--------------------

1) Define your data types in the package.json

``
"galaxy": {
"datatypes": ["sequence.Fasta", "sequences", "msa.clustal"]
}
`

2) Add the galaxy-vis keyword to your package.json


So your keyword list could look like this.
`
keywords = ["biojs", "galaxy-vis"]
`

3) Define a custom galaxy.mako (package root)

`
galaxy.getData(response){
galaxy.el.textContent = response;
console.log("datatype", galaxy.dataType);
});
`

4) Check whether you have defined correct sniper settings.

There are some predefined variables in the galaxy namespace.

* url raw URL to your data file
* dataType dataType of your file
* config galaxy config parameters (e.g. id)
* meta galaxy meta information (e.g. timestamps)
* el an existing div for your component
* relativeURL URL to your galaxy vis plugin
* jsonURL URL to your data file (wrapped in a JSON object - only use this if the API throws an error for the raw file

TODO: read more settings like a data provider from the package.json

How does it work
---------------

1) Query npm: "give me all package with the "galaxy-vis tag"
2) For every package (async)
a) Download the package and install its dependencies
b) Browserify the package and copy the output to /static/{{name}}
c) Copy the js and css resources defined in the biojs sniper settings to static (http links are downloaded)
d) Copy the galaxy.mako into a mako template
e) Generate a config file based on the specified data types

How to run
-------------

Install:

`
npm install -g biojs2galaxy
`

Run:

`
biojs2galaxy
`

Specify a specific output folder (default: $(pwd)/build

`
biojs2galaxy
`

(You need npm & node, of course)

How to use
----------

`
Usage: biojs2galaxy [packages]

Automated import of biojs components into galaxy

Options:

-h, --help output usage information
-V, --version output the version number
-v, --verbose Increase verbosity
-a, --all Download all packages from npm
-o, --output [folder] Output folder
-p, --path [path] Path to local package
-r, --remove Clear output folder
`

#### Download packages:

`
biojs2galaxy msa,biojs-vis-sequence
`

#### Download all packages:

`
biojs2galaxy --all
`

#### Local mode (for development):

`
biojs2galaxy -p ../msa
`

How to develop
-----------

`
git clone https://github.com/biojs/biojs2galaxy
cd biojs2galaxy
npm install
node biojs2galaxy.js
``