fastqc: update to 0.11.2

Closes #1072.
R: option to build libRmath only.

Closes #1067.
Abyss 1.5.2

Closes #1065.
ASL: update to 20140718.
R: add explicit paths to readline.
blast: Fails to build with gcc 4.9

error: must #include <typeinfo> before using typeid

Closes #1078
vecfortlib: 0.4.0 - Updated new version

Updated to version 0.4.0, points to new cblas.h location on Mavericks
Fixes issue with sgemv_ when data is not aligned to 8-byte boundaries

Closes #1083.
emboss: skip build time embossupdate

Missing update mirror causing build failure.
pymol: fix patch args and shasum

Fixes #1082.
sextractor: revert "Use patch DSL"
bowtie 1.1.0
trans-abyss 1.5.1
bowtie: avoid staging source files
bowtie: fix bowtie bin symlink
htslib 0.2.0-rc11
samtools: 0.2.0-rc11 devel
atram 1.03: New formula

aTRAM: automated Target Restricted Assembly Method

Closes #1079
ncview: add mirror

Closes #1084.
bwa: Fix test

The test failed on Linux because the test FASTA file was incorrectly formatted.
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes
at bntseq.c line 270
bcftools 0.2.0-rc11

Fixes build issue with already upgraded htslib (chapmanb/bcbio-nextgen#519).
Removes no longer needed htslib version replacement.

Closes #1085.