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