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bdgenomics.mango.pileup

Project description

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

Project details


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Files for bdgenomics.mango.pileup, version 0.0.5
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Filename, size bdgenomics.mango.pileup-0.0.5-py3.7.egg (1.8 MB) File type Egg Python version 3.7 Upload date Hashes View hashes
Filename, size bdgenomics.mango.pileup-0.0.5.tar.gz (892.4 kB) File type Source Python version None Upload date Hashes View hashes

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