bdgenomics.mango.pileup 0.0.5
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Description:
bdgenomics.mango.pileup 0.0.5
bdgenomics.mango.pileup
bdgenomics.mango.pileup is a Jupyter widget that allows users to view genomic reads, variants and features in a python notebook.
bdgenomics.mango.pileup builds off of pileup.js.
Installation
from pip:
$ pip install bdgenomics.mango.pileup
$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup # can be skipped for notebook version 5.3 and above
from Source:
For a development installation (requires npm >= 3.10.10 and node.js >= 6.11.0),
$ git clone https://github.com/bdgenomics/mango
$ cd mango-viz
$ rm -r bdgenomics/mango/pileup/static
Install bdgenomics.mango.pileup:
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup
After pileup.js is installed once, you can just run the following for development:
$ cd mango-viz
$ rm -r bdgenomics/mango/pileup/static/
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
$ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup
For running examples:
$ First run installation, explained above.
$ cd examples
$ jupyter notebook
For javascript development type checking:
$ cd js
$ npm run test
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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