GeneValidatorApp

Introduction

This is a online web application for GeneValidator. This app is currently hosted at: genevalidator.sbcs.qmul.ac.uk.

GeneValidator helps in identifing problems with gene predictions and provides useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.

If you use GeneValidator in your work, please cite us as follows:

Dragan M^‡, Moghul MI^‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.

Installation

Installation Requirements

Ruby (>= 2.0.0)
NCBI BLAST+ (>= 2.2.30+) (download here).
MAFFT installation (>=7.273) (download here).

Please see here for more help with installing the prerequisites.

Installation

Simply run the following command in the terminal.

gem install genevalidatorapp

If that doesn't work, try sudo gem install genevalidatorapp instead.

Running From Source (Not Recommended)

It is also possible to run from source. However, this is not recommended.

# Clone the repository.
git clone https://github.com/wurmlab/genevalidatorapp.git

# Move into GeneValidatorApp source directory.
cd GeneValidatorApp

# Install bundler
gem install bundler

# Use bundler to install dependencies
bundle install

# Optional: run tests and build the gem from source
bundle exec rake

# Run GeneValidator.
bundle exec genevalidatorapp -h
# note that `bundle exec` executes GeneValidatorApp in the context of the bundle

# Alternativaly, install GeneValidatorApp as a gem
bundle exec rake install
genevalidatorapp -h

Launch GeneValidator

To configure and launch GeneValidatorApp, run the following from a command line.

genevalidatorapp

GeneValidatorApp will automatically guide you through an interactive setup process to help locate BLAST+ binaries and ask for the location of BLAST+ databases.

That's it! Open http://localhost:4567/ and start using GeneValidator!

Advanced Usage

See $ genevalidatorapp -h for more information on all the options available when running GeneValidatorApp.

SUMMARY:
  GeneValidator - Identify problems with predicted genes

USAGE:
  $ genevalidatorapp [options]

Examples:
  # Launch GeneValidatorApp with the given config file
  $ genevalidatorapp --config ~/.genevalidatorapp.conf

  # Launch GeneValidatorApp with 8 threads at port 8888
  $ genevalidatorapp --num_threads 8 --port 8888

  # Create a config file with the other arguments
  $ genevalidatorapp -s -d ~/database_dir

    -c, --config_file                Use the given configuration file
    -b, --bin                        Load BLAST+ and/or MAFFT binaries from this directory
    -d, --database_dir               Read BLAST database from this directory
    -f, --default_database_path      The path to the default BLAST database
    -n, --num_threads                Number of threads to use to run a BLAST search
    -r, --require                    Load extension from this file
    -H, --host                       Host to run GeneValidatorApp on
    -p, --port                       Port to run GeneValidatorApp on
    -s, --set                        Set configuration value in default or given config file
    -l, --list_databases             List BLAST databases
    -D, --devel                      Start GeneValidatorApp in development mode
    -v, --version                    Print version number of GeneValidatorApp that will be loaded
    -h, --help                       Display this help message.

Using Docker

# With protein database files inside a folder named db
docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/genevalidator

This program was developed at Wurm Lab, QMUL with the support of a BBSRC grant.