README.md in genevalidatorapp-1.5.1 vs README.md in genevalidatorapp-1.5.2
- old
+ new
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# GeneValidatorApp
[](https://travis-ci.org/wurmlab/genevalidatorapp)
-[](http://badge.fury.io/rb/GeneValidatorApp)
-[](https://gemnasium.com/wurmlab/GeneValidatorApp)
-[](https://scrutinizer-ci.com/g/wurmlab/GeneValidatorApp/?branch=master)
+[](http://badge.fury.io/rb/genevalidatorapp)
+[](https://scrutinizer-ci.com/g/wurmlab/genevalidatorapp/?branch=master)
-This is a Sinatra based web wrapper for [GeneValidator](https://github.com/monicadragan/GeneValidator); a program that validates gene predictions. A working example can be seen at [genevalidator.sbcs.qmul.ac.uk](http://genevalidator.sbcs.qmul.ac.uk).
-If you use this program in your research, please cite us as follows:
-"Dragan M, Moghul MI, Priyam A & Wurm Y (<em>in prep</em>) GeneValidator: identify problematic gene predictions"
-This program was developed at [Wurm Lab](http://yannick.poulet.org), [QMUL](http://sbcs.qmul.ac.uk) with the support of a BBSRC grant.
+
+
+## Introduction
+
+This is a online web application for [GeneValidator](https://github.com/wurmlab/genevalidator). This app is currently hosted at: [genevalidator.sbcs.qmul.ac.uk](http://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<sup>‡</sup>, Moghul MI<sup>‡</sup>, Priyam A, Bustos C & Wurm Y (<em>in prep.</em>) GeneValidator: identify problematic gene predictions"
+
+
+
+
+
+
+-
## Installation
+### Installation Requirements
+* Ruby (>= 2.0.0)
+* NCBI BLAST+ (>= 2.2.30+) (download [here](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)).
+* MAFFT installation (download [here](http://mafft.cbrc.jp/alignment/software/)).
-1) Install all GeneValidator Prerequisites (ruby <= 2.0.0, Mafft, BLAST+). You would also require a BLAST database.
- * Please see [here](https://gist.github.com/IsmailM/b783e8a06565197084e6) for more information.
+Please see [here](https://gist.github.com/IsmailM/b783e8a06565197084e6) for more help with installing the prerequisites.
-2) Install GeneValidatorApp
+### Installation
+Simply run the following command in the terminal.
- $ gem install genevalidatorapp
+```bash
+gem install genevalidatorapp
+```
-## Usage
+If that doesn't work, try `sudo gem install genevalidatorapp` instead.
-After installing simply type in:
+##### Running From Source (Not Recommended)
+It is also possible to run from source. However, this is not recommended.
- $ genevalidatorapp
+```bash
+# Clone the repository.
+git clone https://github.com/wurmlab/genevalidatorapp.git
-and then go to [http://localhost:4567](http://localhost:4567) (if on a local server and using the default port: 4567)
+# Move into GeneValidatorApp source directory.
+cd GeneValidatorApp
-See `$ genevalidator -h` for more information on how to run GeneValidatorApp.
+# Install bundler
+gem install bundler
- USAGE
-
- genevalidatorapp [options]
-
- Example
-
- # 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
+# Use bundler to install dependencies
+bundle install
- # Create a config file with the other arguments
- $ genevalidatorapp -s -d ~/database_dir
-
- Compulsory (unless set in a config file)
- -d, --database_dir Read BLAST database from this directory
-
- Optional
- -f, --default_db The Path to the the default database
- -n, --num_threads Number of threads to use to run a BLAST search
- -c, --config_file Use the given configuration file
- -r, --require Load extension from this file
- -p, --port Port to run GeneValidatorApp on
- -s, --set Set configuration value in default or given config file
- -l, --list_databases List BLAST databases
- -b, --blast_bin Load BLAST+ binaries from this directory
- -m, --mafft_bin Load Mafft binaries from this directory
- -D, --devel Start GeneValidatorApp in development mode
- -v, --version Print version number of GeneValidatorApp that will be loaded
- -h, --help Display this help message.
+# 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
-## Setting up a Config File
+# Alternativaly, install GeneValidatorApp as a gem
+bundle exec rake install
+genevalidatorapp -h
+```
-GeneValidatorApp requires a number of arguments in order to work. You can either provide these variables to the app through a config file or through command line arguments.
-In order to create a config file, run genevalidator with the `-s` or `--set` argument as follows.
- $ genevalidator -s -d database_dir -f default_db -n num_threads -p port -b blast_bin -m mafft_bin
-The `--set` argument create a config file at `~/.genevalidatorapp.conf` using all the other arguments used. Thereafter, GeneValidatorApp will read the config file before starting the app. This means that you are not required provide the same arguments again and again.
+## Launch GeneValidator
-### Config file
+To configure and launch GeneValidatorApp, run the following from a command line.
-A config file can also be set up manually. Below is an example:
+```bash
+genevalidatorapp
+```
- :database_dir: "/Users/ismailm/blastdb"
- :default_db: "/Users/ismailm/blastdb/SwissProt"
- :web_dir: "/Users/ismailm/GV"
- :num_threads: 8
- :port: 4567
- :host: localhost
- :devel: true
- :blast_bin: "/Users/ismailm/blast/bin"
- :mafft_bin: "/Users/ismailm/mafft/bin"
+GeneValidatorApp will automatically guide you through an interactive setup process to help locate BLAST+ binaries and ask for the location of BLAST+ databases.
-## API
+That's it! Open http://localhost:4567/ and start using GeneValidator!
-See [GeneValidatorApp-API](https://github.com/IsmailM/GeneValidatorApp-API) for more information.
-## Contributing
-1. Fork it ( https://github.com/wurmlab/GeneValidatorApp/fork )
-2. Create your feature branch (`git checkout -b my-new-feature`)
-3. Commit your changes (`git commit -am 'Add some feature'`)
-4. Push to the branch (`git push origin my-new-feature`)
-5. Create a new Pull Request
+
+
+
+## Advanced Usage
+
+See `$ genevalidatorapp -h` for more information on all the options available when running GeneValidatorApp.
+
+```bash
+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.
+```
+
+
+<hr>
+
+This program was developed at [Wurm Lab](https://wurmlab.github.io), [QMUL](http://sbcs.qmul.ac.uk) with the support of a BBSRC grant.