Installing and Configuring SnpEff
=================================

MiModD can use SnpEff (v3.3 through 4.0) during variant annotation. 

.. Warning::

   Version 0.1.5.1 of MiModD supports SnpEff v4.0, but NOT v4.1, which 
   introduced a change in SnpEff variant annotation. We are planning to support
   v4.1 with the next release of MiModD.
   
Installation of SnpEff is optional (though we recommend making use of this 
option) and can be done at any time, i.e. you do not have to have SnpEff to 
install MiModD.

.. admonition:: additional requirement
    
   SnpEff is written in and, thus, requires Java, which you may need to
   install separately.

You can **download** SnpEff from `<http://snpeff.sourceforge.net/>`__.

To **install** it, simply unpack the downloaded archive to a newly created 
``snpEff`` folder in your home directory or, if you prefer a different 
installation directory, read the instructions at 
`<http://snpeff.sourceforge.net/download.html#install>`__.

To **activate** SnpEff-dependent functionality of MiModD, you will have 
to configure the SNPEFF_PATH parameter in MiModD (see `Configuring MiModD 
for your system <INSTALL.html#configuring-mimodd-for-your-system>`__).

MiModD does (intentionally) NOT support SnpEff's database on-demand 
download feature. This means that you will have to install SnpEff genome 
files manually before you can use them.

The procedure to do so is explained `here 
<http://snpeff.sourceforge.net/download.html#databases>`__ in the SnpEff 
Documentation. 

One way to learn about which SnpEff genome files are available for download 
suggested by the manual is through the command line via 
(assuming you are running this from the directory you installed SnpEff to)::

  java -jar snpEff.jar databases
  
but since this will list all available downloads (> 20000 according to the 
manual), we recommend using::

  java -jar snpEff.jar databases | grep "your search term for your organism"
  
For example, at the time of writing and for the installed version of 
SnpEff, the output of::

  java -jar snpEff.jar databases | grep "elegans"
  
, which may be used to search for available genome files for *C. elegans*, 
was (with line-wrapping removed)::

  GCA_000162475.1.18    Granulicatella_elegans_atcc_700633          http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GCA_000162475.1.18.zip
  GCA_000162475.1.21    Granulicatella_elegans_atcc_700633          http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GCA_000162475.1.21.zip
  WBcel215.68           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.68.zip
  WBcel215.69           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.69.zip
  WBcel215.70           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel215.70.zip
  WBcel235.18           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.18.zip
  WBcel235.21           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.21.zip
  WBcel235.71           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.71.zip
  WBcel235.72           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.72.zip
  WBcel235.73           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.73.zip
  WBcel235.74           Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.74.zip
  WBcel235.75           Caenorhabditis_elegans                OK    http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WBcel235.75.zip
  WS220.64              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.64.zip
  WS220.65              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.65.zip
  WS220.66              Caenorhabditis_elegans                      http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS220.66.zip
  WS241                 C. elegans                                  http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_WS241.zip

Then, following the documentation, to install the latest genome version 
file you could either run::

  java -jar snpEff.jar download WS241
  
or visit the download link for this version and extract the downloaded 
archive in the ``data`` subfolder of your SnpEff installation.