academic/hyphy: Added (Hypothesis Testing using Phylogenies).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

5 files changed, 216 insertions, 0 deletions

diff --git a/academic/hyphy/README b/academic/hyphy/README
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+HyPhy: Hypothesis testing using Phylogenies
+
+HyPhy is an open-source software package for the analysis of genetic
+sequences (in particular the inference of natural selection) using
+techniques in phylogenetics, molecular evolution, and machine learning.
+It features a rich scripting language for limitless customization of
+analyses. Additionally, HyPhy features support for parallel computing
+environments (via message passing interface).
+
+HyPhy was designed to allow the specification and fitting of a broad
+class of continuous-time discrete-space Markov models of sequence
+evolution. To implement these models, HyPhy provides its own scripting
+language - HBL, or HyPhy Batch Language, which can be used to develop
+custom analyses or modify existing ones. Importantly, it is not
+necessary to learn (or even be aware of) HBL in order to use HyPhy, as
+most common models and analyses have been implemented for user
+convenience. Once a model is defined, it can be fitted to data (using a
+fixed topology tree), its parameters can be constrained in user-defined
+ways to test various hypotheses (e.g. is rate1 > rate2), and simulate
+data from. HyPhy primarily implements maximum likelihood methods, but
+it can also be used to perform some forms of Bayesian inference (e.g.
+FUBAR), fit Bayesian graphical models to data, run genetic algorithms to
+perform complex model selection.
+
+Features
+- Support for arbitrary sequence data, including nucleotide, amino-acid,
+  codon, binary, count (microsattelite) data, including multiple
+  partitions mixing differen data types.
+- Complex models of rate variation, including site-to-site, branch-to-
+  branch, hidden markov model (autocorrelated rates), between/within
+  partitions, and co-varion type models.
+- Fast numerical fitting routines, supporting parallel and distributed
+  execution.
+- A broad collection of pre-defined evolutionary models.
+- The ability to specify flexible constraints on model parameters and
+  estimate confidence intervals on MLEs.
+- Ancestral sequence reconstruction and sampling.
+- Simulate data from any model that can be defined and fitted in the
+  language.
+- Apply unique (for this domain) machine learning methods to discover
+  patterns in the data, e.g. genetic algorithms, stochastic context free
+  grammars, Bayesian graphical models.
+- Script analyses completely in HBL including flow control, I/O,
+  parallelization, etc.
+
+Registration
+you are highly advised to fill the registration form found at:
+https://veg.github.io/hyphy-site/register/
+
+Citing
+Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
+HyPhy: hypothesis testing using phylogenies.
+Bioinformatics 21(5): 676-679
diff --git a/academic/hyphy/References b/academic/hyphy/References
new file mode 100644
index 0000000000..0c7b457efe
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+++ b/academic/hyphy/References
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+HyPhy
+Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
+HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5): 676-679
+
+Datamonkey webserver
+Wayne Delport, Art F. Poon, Simon D. W. Frost and Sergei L. Kosakovsky Pond.
+Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 2010 July 29[Epub ahead of print; PMID: 20671151]
+Sergei L. Kosakovsky Pond and Simon D. W. Frost (2005). Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21(10): 2531-2533
+
+Specific methods implemented in HyPhy
+Selection detection (SLAC/FEL/REL) - Sergei L. Kosakovsky Pond and Simon D. W. Frost (2005) Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. Molecular Biology and Evolution 22(5): 1208-1222
+Internal Fixed Effects Likelihood (IFEL) Sergei L Kosakovsky Pond, Simon DW Frost, Zehava Grossman, Michael B Gravenor, Douglas D Richman and Andrew J Leigh Brown (2006). Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Computational Biology 2(6): e62
+TOGGLE - Wayne Delport, Konrad Scheffler and Cathal Seoighe (2008). Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1. PLoS Pathogens 4(12): e1000242.
+Directional Evolution in Protein Sequences (DEPS) Sergei L Kosakovsky Pond, Art FY Poon, Andrew J Leigh Brown and Simon Frost (2008). A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus. Molecular Biology and Evolution 25(9): 1809-1824
+PARRIS - Konrad Scheffler,Darren P. Martin and Cathal Seoighe (2006). Robust inference of positive selection from recombining coding sequences. Bioinformatics 22(20): 2493-2499
+GA-Branch - S.L. Kosakovsky Pond and S.D.W. Frost (2005). A Genetic Algorithm Approach to Detecting Lineage-specific Variation in Selection Pressure. Molecular Biology and Evolution 22(3): 478-485
+Evolutionary Selection Distance (ESD) Sergei L Kosakovsky Pond, Konrad Scheffler, Michael B Gravenor, Art FY Poon and Simon DW Frost (2009).
+Evolutionary Fingerprinting of Genes. Molecular Biology and Evolution 27(3): 520-536
+Spidermonkey/BGM - Art Poon, Fraser Lewis, Sergei Kosakovsky Pond and Simon Frost (2007). An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Computational Biology 3(11): e23
+Codon Model Selection (CMS) - Wayne Delport, Konrad Scheffler, Gordon Botha, Michael B Gravenor, Spencer V. Muse and Sergei L Kosakovsky Pond (2010) CodonTest: modeling amino-acid substitution preferences in coding sequences. PLoS Computational Biology 6(8): e1000885
+Branch-site REL - Sergei L. Kosakovsky Pond1, Ben Murrell, Mathieu Fourment, Simon D. W. Frost, Wayne Delport and Konrad Scheffler (2011)
+A random effects branch-site model for detecting episodic diversifying selection. Molecular Biology and Evolution (first published online June 13, 2011 doi:10.1093/ molbev/msr125)
+MEME - Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S. L. (2012) Detecting Individual Sites Subject to Episodic Diversifying Selection". PLoS Genet, 8(7), e1002764+
+SBP/GARD - Sergei L Kosakovsky Pond, David Posada, Michael B Gravenor, Christopher H Woelk and Simon DW Frost. Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Molecular Biology and Evolution 23(10): 1891-1901
+SCUEAL - Sergei L Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art FY Poon, Gareth Hughes, Esther Fearnhill, Mike B Gravenor, Andrew J Leigh Brown and Simon DW Frost (2009). An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. PLoS Computational Biology 5(11): e1000581
+Ancestral Sequence Reconstruction (ASR) (joint) - Tal Pupko, Itsik Pe'er Ron Shamir and Dan Graur (2000). A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences. Molecular Biology and Evolution 17: 890-896
+ASR (marginal) - Z Yang, S Kumar and M Nei (1995). A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences. Genetics 141: 1641-1650
+ASR (sampled) - Rasmus Nielsen (2002) Mapping mutations on phylogenies. Systematic Biology 51(5): 729-739
diff --git a/academic/hyphy/hyphy.SlackBuild b/academic/hyphy/hyphy.SlackBuild
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+++ b/academic/hyphy/hyphy.SlackBuild
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+#!/bin/sh
+
+# Slackware build script for hyphy
+
+# Copyright 2017 Petar Petrov slackalaxy@gmail.com
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+PRGNAM=hyphy
+VERSION=${VERSION:-2.3.4}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $PRGNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Fix the libraries path on 64 systems
+sed -i "s:lib/hyphy:lib${LIBDIRSUFFIX}/hyphy:g" CMakeLists.txt
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_REQUIRED_FLAGS="$SLKCFLAGS" \
+    -DDEFAULT_COMPILE_FLAGS="$SLKCFLAGS" \
+    -DINSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release ..
+
+# This builds build a HyPhy executable (HYPHYMP) using pthreads to do multiprocessing
+  make MP
+  make install DESTDIR=$PKG
+cd ..
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+# Include a few examples
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a Examples $PKG/usr/share/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a help/*.pdf LICENSE README.md $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References >  $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/hyphy/hyphy.info b/academic/hyphy/hyphy.info
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+PRGNAM="hyphy"
+VERSION="2.3.4"
+HOMEPAGE="https://veg.github.io/hyphy-site/"
+DOWNLOAD="https://github.com/veg/hyphy/archive/2.3.4/hyphy-2.3.4.tar.gz"
+MD5SUM="1377f4973f40c7d336cb8d7c81a0bd34"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/hyphy/slack-desc b/academic/hyphy/slack-desc
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+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+     |-----handy-ruler------------------------------------------------------|
+hyphy: hyphy (Hypothesis Testing using Phylogenies)
+hyphy:
+hyphy: HyPhy is a software package for the analysis of genetic sequences,
+hyphy: in particular the inference of natural selection, using techniques
+hyphy: in phylogenetics, molecular evolution, and machine learning. It
+hyphy: features a rich scripting language for limitless customization of
+hyphy: analyses.
+hyphy:
+hyphy: Home: https://veg.github.io/hyphy-site/
+hyphy:
+hyphy: