pcl: Disable cloud_composer and point_cloud_editor

Qt4 apps are not compatible with boost 1.56, and PCL is not ready
to switch to Qt5 yet.

Fixes #1209.
Closes #1211.
hlaminer: Add dependency to blast

Closes #1206.
vips 7.40.10

Closes #1213.
methpipe 3.3.1 (new formula)

Closes #1207.
ASL: version 20140929.
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.