bowtie2 2.2.4

Closes #1335.
r: Add an additional rJava caveat

To fix 'fatal error: 'jni.h' file not found' after running
'R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers'
as suggested

Closes #1330.
Correct uppercase name on veclibfort

Closes #1340.
New formula: statismo

Closes #1333.
ParaView 4.2.0: New formula

ParaView is an open-source, data analysis and visualization application.

Closes #1244.
ASL: version 20141106.

Closes #1343.
stacks 1.21

Depends on htslib rather than samtools for BAM support.
stacks 1.21: Remove --disable-openmp

It is not necessary to use --disable-openmp with clang 6.0.
infernal 1.1.1: Add tag bioinformatics
qualimap: update to v2.0

Closes #1348.
sailfish 0.6.2: Fails to build with clang 600

Add bioinformatics tag.
jellyfish-1.1: fails with clang

Closes #1354.
bedtools 2.22.0

Closes #1351.
sailfish 0.6.3
Bump fails_with clang

Closes #1355.
zoltan 3.81

New version of Zoltan (3.81).

Closes #1349.
gdcm: add option to build with vtk

Closes #1331.
gdcm: add c++11 option

Closes #1356.
insighttoolkit: add option to build ITK with gdcm

Closes #1332.
gromacs: deprecate options