snoopy 0.4.5

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

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 samtools to be installed and in your path.

Installation

pip install snoopy

Authors

• Daniel Rice ([e-mail])

• Jeff Barrett

Documentation

All documentation is at Read the Docs.

FAQs

On Ubuntu, Failed building wheel for cryptography

Snoopy requires the python package paramiko which in turn requires cryptography. According to this stackoverflow question 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

Development

To install snoopy for development purposes, if you don’t have this already install Node Version Manager and use it 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/.