genomicviz

genomicviz

Installation

For a development installation (requires npm >= 3.10.10 and node.js >= 6.11.0),

$ git clone https://github.com/akmorrow13/genomicviz.git
$ cd genomicviz
$ rm -r genomicviz/static/

Genomicviz uses a version of pileup.js not yet in npm. To install the latest version of pileup:

$ git clone https://github.com/hammerlab/pileup.js.git
$ cd pileup.js
$ npm run build

Navigate to genomicviz:

$ cd js/
$ mkdir node_modules
$ npm install --save <path_to_pileup>
$ cd ..
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix genomicviz
$ jupyter nbextension enable --py --sys-prefix genomicviz

After pileup.js is installed once, you can just run the following for development:

$ cd genomicviz
$ rm -r genomicviz/static/
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix genomicviz
$ jupyter nbextension enable --py --sys-prefix genomicviz

For running examples:

$ First run installation, explained above.
$ cd examples
$ jupyter notebook

For javascript development type checking:

$ cd js
$ npm run test