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

You can find a step for step example guide here.

Install:

npm install -g biojs2galaxy

Run:

biojs2galaxy

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

biojs2galaxy <folder>

(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

biojs / biojs2galaxy

readme