parsnp 1.0: New formula

Rapid bacterial core genome alignment and SNP detection

Closes #1566.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>
parsnp: add 1.0 bottle.
Octave: changle angled includes to quote includes.

This makes it possible for other software to build upon Octave,
e.g., Shogun.

Closes #1561.
mira 4.0.2: Add doi and tag
allpaths-lg 50378: Change single quotes to double
trinity r20131110: Change single quotes to double
amos 3.1.0: Add doi and tag
barrnap 0.5: Remove require "formula"

Closes #1570.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>
barrnap: add 0.5 bottle.
abyss-explorer 1.3.4: Remove require "formula"

Closes #1569.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>
abyss-explorer: add 1.3.4 bottle.
cerulean 0.1: Remove require "formula"

Closes #1571.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>
cerulean 0.1: Requires numpy
gingr 1.0.1: New formula

Gingr is a flexible platform for visualizing and compressing
alignments and phylogenetic trees.

Closes #1564.

Signed-off-by: Shaun Jackman <sjackman@gmail.com>
Squashed commit of the following:

commit f6a43ec5ff8436e2b2eac48d7a347f610adc5bb7
Author: Sebastian Schöps <sebastian@schoeps.org>
Date:   Mon Dec 29 20:19:18 2014 +0100

    Moved onelab.py to libexec/ and changed from "def test" to "test do"

commit 291e0802826992aeaf1091ede1bb2b3a0b079acb
Author: Sebastian Schöps <sebastian@schoeps.org>
Date:   Sun Dec 21 23:36:48 2014 +0100

    cleaned white spaces

commit acffadce9e9cf843ec32d5ee6a51512071a546ed
Author: Sebastian Schöps <sebastian@schoeps.org>
Date:   Tue Dec 16 11:45:15 2014 +0100

    Removed trailing white space and made petsc/slepsc optional

commit df05f6f54ab624417f2513dd38071581b71c0fc5
Author: Sebastian Schoeps <schoeps@gsc.tu-darmstadt.de>
Date:   Sat Nov 29 00:33:45 2014 +0100

    added petsc and opencascade