Version 1.1

Documentation is now self contained.

Ansible instructions are now able to provision a Ubuntu 16.04 machine
where MinVar is correctly installed with all its dependencies.

This commit also closes #7 and closes #8

Author: ozagord

ansible/hosts

@@ -1,2 +1,2 @@
 [minvarmachine]
-172.23.10.194
+XYZ.XYZ.XYZ.XYZ

ansible/setup.retry

@@ -1 +1 @@
-172.23.10.194
+172.23.100.212

ansible/setup.yml

@@ -18,6 +18,10 @@
     #   apt:
     #     upgrade=yes
 
+    - name: Add repo for openjdk-7
+      apt_repository:
+        repo: 'ppa:openjdk-r/ppa'
+
     - name: Install required software
       apt:
         name={{ item }}
@@ -31,7 +35,6 @@
         - bwa
         - cmake
         - cython
-        - default-jre
         - emboss
         - git
         - libfreetype6-dev
@@ -41,6 +44,8 @@
         - libwww-perl
         - make
         - muscle
+        - maven
+        - openjdk-7-jdk
         - pkg-config
         - python-dev
         - python-setuptools
@@ -138,13 +143,33 @@
       args:
         executable: /bin/bash
 
+    - name: Install GATK
+      shell: |
+        if [ ! -e "/usr/local/GATK/GenomeAnalysisTK.jar" ]; then
+            cd /tmp
+            rm -rf gatk-protected
+            git clone --depth=50 --branch=master https://github.com/broadgsa/gatk-protected.git \
+                && cd /tmp/gatk-protected \
+                && git checkout tags/3.3
+            mvn clean install \
+                && sudo mkdir /usr/local/GATK \
+                && sudo install target/GenomeAnalysisTK.jar /usr/local/GATK
+        fi
+      args:
+          executable: /bin/bash
+
     - name: Make picard directory
       file: path=/usr/local/picard-tools state=directory mode=0755
 
     - name: Install picard
-      get_url:
-        url: https://github.com/broadinstitute/picard/releases/download/2.7.1/picard.jar
-        dest: /usr/local/picard-tools/picard.jar
+      shell: |
+        if [ ! -e "/usr/local/picard-tools/picard.jar" ]; then
+            cd /tmp
+            rm -rf picard-tools-1.141
+            wget -q https://github.com/broadinstitute/picard/releases/download/1.141/picard-tools-1.141.zip
+            unzip picard-tools-1.141.zip && \
+                sudo install picard-tools-1.141/picard.jar /usr/local/picard-tools/
+        fi
 
     - name: Change group of /opt
       file:

rtd/license.md

@@ -5,4 +5,5 @@ It is worthy of note that recalibration is done by GATK, which is itself
 subject to a dual purpose [licensing](https://software.broadinstitute.org/gatk/download/licensing.php):
 free for academic non-commercial research activities, subject to a fee for commercial use.
 
-The overall licensing of MinVar is then under definition.
+While you are free to use MinVar without restriction for research purposes, its
+commercial licensing is under definition.

rtd/user-guide/installation.md

@@ -11,13 +11,6 @@ A condensed list of dependencies
 - bwa
 - lofreq
 
-### Install GATK
-
-GATK is not (yet?) included in the instructions below because you need
-to register online [here](https://software.broadinstitute.org/gatk/download/)
-in order to download it. Then, install it in `/usr/local/GATK`. MinVar expects
-to find the Java archive file `/usr/local/GATK/GenomeAnalysisTK.jar`.
-
 ### Setting up with Ansible
 
 The directory [`ansible`](https://github.com/ozagordi/MinVar/tree/master/ansible)
@@ -55,10 +48,9 @@ set up. Good instructions for this task can be found in this
 #### What can go wrong
 
 We assumed that you have an Ubuntu 16.04 available. Most of the stuff will work
-on Ubuntu 14.04, but you need to switch to a newer version of Java provided by
-Oracle in order to run `picard`. You can find
-[here](https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-get-on-ubuntu-16-04)
-a good tutorial on this.
+on Ubuntu 14.04, but you might run into troubles because of different versions
+of Java (you can find a good tutorial on this
+[here](https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-get-on-ubuntu-16-04)).
 
 `UNREACHABLE!` usually means that the private/public key pair does not work.
 You must be able to ssh into the remote machine with this command (edit accordingly)