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biojs2galaxy
Advanced tools
Readme
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
"galaxy": {
"datatypes": ["sequence.Fasta", "sequences", "msa.clustal"]
}
galaxy-vis
keyword to your package.jsonSo your keyword list could look like this.
keywords = ["biojs", "galaxy-vis"]
galaxy.mako
(package root)galaxy.getData(response){
galaxy.el.textContent = response;
console.log("datatype", galaxy.dataType);
});
There are some predefined variables in the galaxy
namespace.
url
raw URL to your data filedataType
dataType of your fileconfig
galaxy config parameters (e.g. id)meta
galaxy meta information (e.g. timestamps)el
an existing div for your componentrelativeURL
URL to your galaxy vis pluginjsonURL
URL to your data file (wrapped in a JSON object - only use this if the API throws an error for the raw fileTODO: read more settings like a data provider from the package.json
galaxy.mako
into a mako templateInstall:
npm install -g biojs2galaxy
Run:
biojs2galaxy
Specify a specific output folder (default: $(pwd)/build
biojs2galaxy <folder>
(You need npm & node, of course)
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
biojs2galaxy msa,biojs-vis-sequence
biojs2galaxy --all
biojs2galaxy -p ../msa
git clone https://github.com/biojs/biojs2galaxy
cd biojs2galaxy
npm install
node biojs2galaxy.js
FAQs
Continous integration of BioJS components into Galay
The npm package biojs2galaxy receives a total of 6 weekly downloads. As such, biojs2galaxy popularity was classified as not popular.
We found that biojs2galaxy demonstrated a not healthy version release cadence and project activity because the last version was released a year ago. It has 1 open source maintainer collaborating on the project.
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