abyss: build dependencies for --HEAD

Building --HEAD requires autoconf, automake and multimarkdown.

Fixes #52
New Formula: LAMMPS

LAMMPS:
"Large-scale Atomic/Molecular Massively Parallel Simulator"

* Lammps binary, library, and python module are installed
* Both serial and mpi parallelized versions are available
* Docs, examples, tools, and benchmark scripts are installed
* All standard packages are installed (2 are currently disabled)
* User packages are available as options (2 are currently disabled)

* Fixes #45 #63
MrBayes: New formula
mrbayes: Fix mpi compile issue, use beagle formula

- Fails with llvm-gcc
- Fix open-mpi to NOT use llvm when mpicc is called
- Installed doc and examples unless --HEAD
beagle: New formula

- Provides: NvidiaCudaRequirement
Ray 2.1.0: New formula

- Uses MPIDependency
- Fails with llvm-gcc
- has a test
Audit and style fixes
petsc: Add formula for PETSc scientific library

Fixes #49
petsc: Minor fix: Too much space
ray: Put binary 'Ray' in correct place
beagle: Disable JNI, Enable OpenCL
beagle: Fix JNI (Java) bindings.

- Java bindings are installed, if the JDK is available.
  Please note, beagle fails to find necessary headers
  (jni_md.h), because they are in a subdir "darwin" for the JDK
  installed from the Oracle DMG.
- Java bindings need `ENV.deparallelize`. Fixes #67
New formula: bitseq.

BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an
application for inferring expression levels of individual transcripts
from sequencing (RNA-Seq) data and estimating differential expression
(DE) between conditions.

Fixes #50 #46
picard-tools: Added picard tools (JAR) files.

Fixes #51
beagle: white space fix
soapdenovo: New formula SOAPdenovo 1.05

Fixes #54
fermi: New formula Fermi 1.1

Fixes #55
sga: 0.9.37
sga: deactivated --HEAD due to build err
bamtools: Disabled --HEAD, because our patch fails there