Merge pull request #13 from ckennedy-nmdp/new-feature-branch

Process unpaired (SRA) data
Merge branch 'master' of https://github.com/nmdp-bioinformatics/pipeline into new-feature-branch
improving error message on TOOLDIR setting.  Fixes issue #11
Merge pull request #15 from janders3-nmdp/fix_splitter_abort

improving error message on TOOLDIR setting.  Fixes issue #11
creation of prep_data_dir, dependant on presence of /opt/data/tutorial/fastq.  fixes Issue #12
Merge pull request #16 from janders3-nmdp/tutorial_data_dir

creation of prep_data_dir, dependant on presence of /opt/data/tutorial/f...
Merge pull request #14 from ckennedy-nmdp/new-feature-branch

Filter groovy script (Sorry Michael)
necessary path fixes
Merge pull request #18 from janders3-nmdp/update_path_to_ngstools

necessary path fixes
adding license header, style fixes
one less 'reference'
Merge pull request #21 from janders3-nmdp/typo_fix

one less 'reference'
update picard dependency to htsjdk version 1.118
Merge pull request #20 from mheuer-nmdp/style-fixes

Adding license header, style fixes
change builder access methods to withStart() and withEnd()
Merge pull request #24 from ckennedy-nmdp/test-branch

change builder access methods to withStart() and withEnd()
Merge pull request #22 from mheuer-nmdp/update-htsjdk

Update picard dependency to htsjdk version 1.118
do notuse system /tmp, user ~/tmp
Merge pull request #28 from janders3-nmdp/user_specific_tmpdir

do notuse system /tmp, user ~/tmp
adding Travis CI configuration with no-op build script