Metadata-Version: 2.0
Name: snoopy
Version: 0.4.3
Summary: Browser based quality control tool to expedite reviewing predicted variants in next generation sequencing files.
Home-page: https://github.com/wtsi-medical-genomics/snoopy
Author: Daniel Rice
Author-email: dr9@sanger.ac.uk
License: MIT
Keywords: quality control qc variants next generation sequencing bam cram
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS
Classifier: Environment :: Web Environment
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Dist: paramiko
Requires-Dist: tornado

######
Snoopy
######

Browser based quality control tool to expedite reviewing predicted variants in next generation sequencing files.

************
Requirements
************

Snoopy has been tested on

* Mac OS X
* Ubuntu

And requires

* python (2 or 3)
* a modern web browser

If your files reside on a server without HTTP/S access snoopy can access this but will require a **samtools** to be installed and in your path.

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Installation
************


FAQs
====

On Ubuntu, Failed building wheel for cryptography
-------------------------------------------------

Snoopy requires the python package paramiko which in turn requires cryptography. According to `this stackoverflow question <http://stackoverflow.com/questions/22073516/failed-to-install-python-cryptography-package-with-pip-and-setup-py>`_ in order to install cryptography on Debian and Ubuntu you must first::

    sudo apt-get install build-essential libssl-dev libffi-dev python-dev

and on Fedora and RHEL-derivatives::

    sudo yum install gcc libffi-devel python-devel openssl-devel


On Ubuntu, npm start fails with Error: watch ENOSPC
---------------------------------------------------

According to https://discourse.roots.io/t/gulp-watch-error-on-ubuntu-14-04-solved/3453 this is caused by a limit for how many files can be watched by a user and can be updated with::

	echo fs.inotify.max_user_watches=582222 | sudo tee -a /etc/sysctl.conf && sudo sysctl -p


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Authors
*******

* Daniel Rice (dr9@sanger.ac.uk)
* Jeff Barrett


*************
Documentation
*************

All documentation is at `Read the Docs <http://snoopy.readthedocs.io/>`_.


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Development
***********

To install snoopy for development purposes, if you don't have this already install `Node Version Manager <https://github.com/creationix/nvm>`_. Use **NVM** to install v4.4.5 of Node::

	$ nvm install v.4.4.5
	$ nvm use v4.4.5

Clone the repository::

	$ git clone --recursive https://github.com/wtsi-medical-genomics/snoopy.git

Build dalliance::

	$ cd snoopy/snoopy/dalliance
	$ npm install -g gulp
	$ npm install
	$ gulp

Build snoopy::

	$ cd .. // now in snoopy/snoopy/
	$ npm install
	$ npm start


*******
License
*******

Copyright (c) 2016 Genome Research Ltd.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.


