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.
APL: new formula.
ASL: update to 20140723.

Closes #1088.
JBLAS: new formula.
cantera: new formula for Cantera 2.1

Closes #1090.
Cuba: new formula

Closes #1089.
Veclibfort: fails for OSX <= 10.6

The failure is due to missing LAPACK symbols in the vecLib framework.

Fixes #1074.
new formula: openni2 2.2.0.33

Closes #1076.
trans-abyss: python-igraph requires igraph
daligner 2014-07-10: New formula

Find all significant local alignments between reads
barrnap 0.5
prokka 1.10
Netcdf: Add mirrors for two resources.

Closes #1092.
lumpy-sv: v0.2.4 and de-parallelize

Update to latest lumpy version (with Perl scripts for speedseq
compatibility) and de-parallelize make file to try and avoid issues
building on CentOS5 with gcc-4.1

Closes #1096.
minc: bump fails_with clang

Fixes #1095.
fasta: Add DOI
kissplice 2.2.1
root: upgrade to 5.34.19, workaround ROOT-5773

https://sft.its.cern.ch/jira/browse/ROOT-5773

Fixes #1094.
Closes #1098.
picard-tools 1.118

Closes #1099.