SGA 0.9.42

HEAD once again builds with clang, since jts/sga#35 is fixed.

Closes #74
velvet: option to support longer kmers

Velvet is usually built to support a maximum kmer size of either 31 or 63
and this patch adds a '--with-63mer' option to build the latter.
trinity: new formula: Trinity r2012-10-05

De novo transcriptome assembler for RNA-Seq data
fastqc: new formula: FastQC 0.10.1

A quality control tool for high throughput sequence data.
raxml: new formula: RAxML 7.2.8-ALPHA

Randomized Axelerated Maximum Likelihood is a program for sequential and
parallel Maximum Likelihood based inference of large phylogenetic trees.
gblocks: new formula: Gblocks 0.91b

Selection of conserved blocks from multiple alignments for their use
in phylogenetic analysis
macse: new formula: MACSE 0.9b1

MACSE: Multiple Alignment of Coding SEquences Accounting for
Frameshifts and Stop Codons
Merge branch 'gblocks'
Merge branch 'trinity'
Merge branch 'fastqc'
Merge branch 'raxml'
seqdb: new formula: SeqDB 0.2.0

A file format, compressor and storage tool for the raw data produced by
Next-Generation Sequencing platforms.
Merge branch 'seqdb'
velvet: option to support longer kmers (alternate)

Uses the values of the MAXKMERLENGTH env. var. instead of a --with option.
bowtie2: updated version to 2.0.6
bowtie: updated version to 0.12.9
velvet: bugfix: sha1 changed

The file http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz
was replaced with a different version on the server.
oases: new formula: Oases 0.2.08

A de novo transcriptome assembler for very short reads
Merge branch 'oases'
Merge branch 'velvet'