Update version and rank model

docs/index.rst

@@ -25,6 +25,7 @@ Contents:
    structure
    vcfParser
    qcCollect
+   rank_modelv1.12
    rank_modelv1.11
    rank_modelv1.5
    configuration_file

docs/installation.rst

@@ -1,6 +1,58 @@
 Installation
 ==============
 
+Automated Installation
+~~~~~~~~~~~~~~~~~~~~~~
+This installation procedure assumes that you have a working perl version and a `Miniconda`_
+installation.
+
+1. "Install" MIP
+
+  .. code-block:: console
+    
+    clone the official git repository
+    $ git clone https://github.com/henrikstranneheim/MIP.git
+    $ cd MIP
+
+  After this you can decide whether to make MIP an "executable" by either adding the install directory to the ``$PATH`` in e.g. "``~/.bash_profile``" or move all the files from this directory to somewhere already in your path like "``~/usr/bin``". 
+  Remember to make the file(s) executable by ``chmod +x file``.
+
+2. Create the install instructions for MIP
+
+  .. code-block:: console
+  
+    $ perl install.pl
+    This will generate a batch script "mip.sh" for the install in your working directory.
+    
+3. Run the bash script
+
+  .. code-block:: console
+ 
+    $ . mip.sh
+    This will install all the dependencies of MIP and other modules included in MIP into a conda environment (defaults to "mip"). 
+    However a fresh version of perl and cpanm is installed outside of the conda environment, but are activated through bashrc and  bash_profile.
+
+.. note::
+
+  This will add the following lines to bashrc and bash_profile if the install perl version 
+  is not found in your path:
+
+  .. code-block:: console
+  
+     'export PATH=$HOME/perl-PERLVERSION/:$PATH' >> ~/.bashrc
+     'eval `perl -I ~/perl-PERLVERSION/lib/perl5/ -Mlocal::lib=~/perl-PERLVERSION/`' >> ~/.bash_profile
+
+3. Run MIP
+
+  .. code-block:: console
+    
+    $ source activate mip
+    $ perl mip.pl -h
+
+
+Manual Installation
+~~~~~~~~~~~~~~~~~~~~
+
 1. Install a fresh copy of Perl
 
   On UNIX, Perl5 can be installed by following these `instructions <http://learn.perl.org/installing/unix_linux.html>`_. It uses `Perlbrew <http://perlbrew.pl/>`_.
@@ -34,4 +86,6 @@ Installation
   .. code-block:: console
     
     cpanm <dependency>
-    $ cpanm YAML
+    $ cpanm YAML
+
+.. _Miniconda: http://conda.pydata.org/miniconda.html

docs/setup.rst

@@ -22,23 +22,25 @@ are tested for compatibility with MIP.
 
 **Program/Modules**
 
-- Perl `YAML.pm`_ module and `Log::Log4perl.pm`_ since this is not included in the Perl standard
-  distribution
+- Perl modules: YAML.pm, Log4perl.pm, List::MoreUtils, DateTime, DateTime::Format::ISO8601, 
+  DateTime::Format::HTTP, DateTime::Format::Mail, Set::IntervalTree from CPAN, since these
+  are not included in the perl standard distribution
 - Simple Linux Utility for Resource Management (`SLURM`_)
 - `FastQC`_ (version: 0.11.2)
 - `Mosaik`_ (version: 2.2.24)
 - `BWA`_ (version: 0.7.12)
-- `SAMTools`_ (version: 1.1)
-- `BedTools`_ (version: 2.20.1)
-- `PicardTools`_ (version: 1.137)
-- `Chanjo`_ (version: 2.3.0)
+- `Sambamba`_ (version: 0.5.9)
+- `SAMTools`_ (version: 1.2)
+- `BedTools`_ (version: 2.25.0)
+- `PicardTools`_ (version: 1.139)
+- `Chanjo`_ (version: 3.1.0)
 - `GATK`_ (version: 3.4-46)
 - `VT`_ (version: 0.5)
-- `VEP`_ (version: 81)
+- `VEP`_ (version: 82)
 - vcfParser.pl (Supplied with MIP; see :doc:`vcfParser`)
 - `SnpEff`_ (4.1)
 - `ANNOVAR`_ (version: 2013-08-23)
-- `GENMOD`_ (version: 3.0.1)
+- `GENMOD`_ (version: 3.4.0)
 - `VcfTools`_ (version: 0.1.12b)
 - `BcfTools`_ (version: 1.1)
 - `PLINK`_ (version: 1.07)
@@ -121,12 +123,11 @@ directory using Annovars built-in download function.
    This applies only to the supported annovar databases. Supply flag "--annovarSupportedTableNames"
    to list the MIP supported databases.
 
-.. _YAML.pm: http://search.cpan.org/~mstrout/YAML-0.84/lib/YAML.pm
-.. _Log::Log4perl.pm: http://search.cpan.org/~mschilli/Log-Log4perl-1.46/lib/Log/Log4perl.pm
 .. _Mosaik: https://github.com/wanpinglee/MOSAIK
 .. _BWA: http://bio-bwa.sourceforge.net/
 .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 .. _SAMtools: http://samtools.sourceforge.net/
+.. _Sambamba: http://lomereiter.github.io/sambamba/
 .. _BedTools: http://bedtools.readthedocs.org/en/latest/
 .. _SLURM: http://slurm.schedmd.com/
 .. _PicardTools: http://picard.sourceforge.net/