edirect 2.00: Update SHA1

Was 7f30f659f58c4bb77b87e514042fd415d226fc9a
Now c77a311486816966456712b2117503fea4aaa1a8
maker 2.31.5: repeatmasker, snap are recommended

Depends on DBD::Pg
Fix Inline::C dependency
maker 2.31.5: DBD::Pg is optional
maker 2.31.6
ogdraw 1.1.1: Add patch for --gc option
gdcm 2.4.4

Closes #1212.
tophat 2.0.13

Closes #1223.
nextflow 0.10.3

Closes #1224.
ASL: 20141003

Fixes #1227.
veclibfort: update to 0.4.2

vecLibFort now works with Leopard, even PPC Leopard. This has been accomplished without breaking compatibility with newer versions of OSX.

Closes #1232.
opencv: fix CUDA support

Closes #1228.
Closes #970.
Fixes #1182.
mrbayes: comment out ENV setting with mpi

open-mpi has been updated to 1.8, which doesn't use llvm-gcc to do
compiling the comment about the hang doesn't apply anymore.

Closes #1226.
ASL: 20141004

Closes #1237.
osgearth: build open-scene-graph with Qt

Fixes #1238.
edirect: update sha1
vips 7.40.11

Closes #1239.
fsa 1.15.9: New formula

FSA is a probabilistic multiple sequence alignment algorithm which uses a
distance-based approach to aligning homologous protein, RNA or DNA sequences.
blast 2.2.29: Fails to build with clang build 600

Closes #1078
pcl: add patch for boost 1.56

Enables cloud_composer and point_cloud_editor
Using WITH_QT to disable qt support

Closes #1241.
octave: build with clang 3.5

Fixes #1193.
Closes #1246.