GeneValidatorApp & GeneValidator Dependencies Installation

GeneValidator_dependencies.md

#Dependencies

GeneValidatorApp and GeneValidator have a number of dependencies (including Ruby, Mafft & BLAST) that need to be installed first.

##Ruby (>= 2.0.0)

1. Install Ruby Version Manager

$ curl -sSL https://get.rvm.io | bash -s stable --ruby
$ source ~/.rvm/scripts/rvm
$ rvm use ruby

If the above fails, due to lack of sudo, attempt the following:

$ curl -L https://get.rvm.io | bash -s -- --ignore-dotfiles --autolibs=0 --ruby
$ source ~/.rvm/scripts/rvm
$ rvm use ruby

##Mafft Installation (>=7.273)

####Mac Users:

1. Download the Mac Package
   http://mafft.cbrc.jp/alignment/software/mafft-7.273-signed.pkg

####Linux Users:

1. Download the right Linux Package (and install)
   http://mafft.cbrc.jp/alignment/software/linux.html

####Usage

1. Check the success of the installation by typing which mafft. This should return a full path to where mafft is installed.

The linux and MacOS Packages will automatically configure your system (i.e. add mafft to you $PATH) so that GeneValidatorApp or GeneValidator are able to find mafft automatically.

##BLAST Installation (>= 2.2.30+)

1. Download the right version of BLAST
   MacOS - ftp://ftp.ncbi.nlm.nih.gov//blast/executables/blast%2B/2.2.30/ncbi-blast-2.2.30%2B-universal-macosx.tar.gz
   Linux - ftp://ftp.ncbi.nlm.nih.gov//blast/executables/blast%2B/2.2.30/ncbi-blast-2.2.30%2B-ia32-linux.tar.gz
   Other Versions - ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/

2. Uncompress
   $ tar zxvpf ncbi-blast+2.2.29-x64-linux.tar.gz

3. Add bin folder to $PATH
   $ export PATH=”$PATH:$HOME/ncbi-blast-2.2.29+/bin

4. Check if it works by typing which blastp

##GSL (GNU Scientific Library) Installation

1. Install using package managers:
   

Mac

$ brew install gsl

Linux

$ sudo apt-get install -y libgsl0-dev

GeneValidator Installation

After installing all the dependencies, please install genevalidator as follows:

$ gem install genevalidator