Add an (unsatisfied) gatk2 package requirement.

This is useful for system administrators which need to load modules
(e.g. JDK 1.7) by adding appropriate commands to
<tool_dependencies_dir>/gatk2/default/env.sh .
Merge pull request #26 from nsoranzo/master

Add package_minced_0_1_4 .
Merge pull request #27 from nsoranzo/gatk2

Add an (unsatisfied) gatk2 package requirement.
added exparna
fixed exparna bug and added twistdna
added a few things
added missing env variable
modified twistdna installation
export ROOT_DIR in addition
finished exparna
added twistdna
added rnaz
Merge pull request #28 from bernhardlutz/master

Vienna RNA
add bedtools tool dependency
change bedtools to bedtools2
add first version of diffbind
fixes for diffbind
small fixes
removing threads and num_cpu_threads_per_data_thread from tools that did not support it
merge