New port, biology/hyphy: Hypothesis testing using Phylogenies

WWW: http://www.hyphy.org/

7 files changed, 645 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 5cef59a1bcbe..9d1f964956e2 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -42,6 +42,7 @@
     SUBDIR += grappa
     SUBDIR += hmmer
     SUBDIR += htslib
+    SUBDIR += hyphy
     SUBDIR += iolib
     SUBDIR += iqtree
     SUBDIR += jalview
diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
new file mode 100644
index 000000000000..6c12aca10b65
--- /dev/null
+++ b/biology/hyphy/Makefile
@@ -0,0 +1,21 @@
+# $FreeBSD$
+
+PORTNAME=	hyphy
+DISTVERSION=	2.3.12
+CATEGORIES=	biology
+
+MAINTAINER=	jrm@FreeBSD.org
+COMMENT=	Hypothesis testing using Phylogenies
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+ONLY_FOR_ARCHS=	amd64 i386
+
+LIB_DEPENDS=	libcurl.so:ftp/curl
+
+USES=		compiler:c++14-lang cmake:outsource localbase:ldflags ssl
+USE_GITHUB=	yes
+GH_ACCOUNT=	veg
+
+.include <bsd.port.mk>
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
new file mode 100644
index 000000000000..be8766d924bd
--- /dev/null
+++ b/biology/hyphy/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1525983314
+SHA256 (veg-hyphy-2.3.12_GH0.tar.gz) = f78d5e7bcab2ad8405b9da9bdb4c7893ad7cd3290e1eec749855b064c6fc60fd
+SIZE (veg-hyphy-2.3.12_GH0.tar.gz) = 7901009
diff --git a/biology/hyphy/files/patch-src_core_calcnode.cpp b/biology/hyphy/files/patch-src_core_calcnode.cpp
new file mode 100644
index 000000000000..8b8dfab80e8f
--- /dev/null
+++ b/biology/hyphy/files/patch-src_core_calcnode.cpp
@@ -0,0 +1,11 @@
+--- src/core/calcnode.cpp.orig	2018-05-10 18:06:35 UTC
++++ src/core/calcnode.cpp
+@@ -5932,7 +5932,7 @@ void    _TheTree::TreePSRecurse (node<no
+         res << "0 0 0 setrgbcolor\n";
+     }
+ 
+-    if (iterator->is_root() == nil && layout == 1) {
++    if (!iterator->is_root() && layout == 1) {
+         res <<  (_String (-iterator->in_object.h) & ' ' & _String (-iterator->in_object.v) & " translate\n");
+     }
+ }
diff --git a/biology/hyphy/files/patch-src_core_regex.cpp b/biology/hyphy/files/patch-src_core_regex.cpp
new file mode 100644
index 000000000000..0520c9be017f
--- /dev/null
+++ b/biology/hyphy/files/patch-src_core_regex.cpp
@@ -0,0 +1,13 @@
+--- src/core/regex.cpp.orig	2018-05-10 18:11:45 UTC
++++ src/core/regex.cpp
+@@ -31,10 +31,6 @@
+ #pragma alloca
+ #endif
+ 
+-#if !defined REGEX_MALLOC && !defined __MINGW32__
+-#include <alloca.h>
+-#endif
+-
+ #ifndef _GNU_SOURCE
+ #define _GNU_SOURCE
+ #endif
diff --git a/biology/hyphy/pkg-descr b/biology/hyphy/pkg-descr
new file mode 100644
index 000000000000..6358bab50caa
--- /dev/null
+++ b/biology/hyphy/pkg-descr
@@ -0,0 +1,9 @@
+HyPhy is an open-source software package for the analysis of genetic sequences
+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, MPI and it can be compiled as a
+shared library and called from other programming environments such as Python and
+R.
+
+WWW: http://www.hyphy.org/
diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist
new file mode 100644
index 000000000000..2b6cb351be73
--- /dev/null
+++ b/biology/hyphy/pkg-plist
@@ -0,0 +1,587 @@
+bin/HYPHYMP
+lib/hyphy/ChartAddIns/Approximate_CDF
+lib/hyphy/ChartAddIns/Column Operations
+lib/hyphy/ChartAddIns/Complex Select Cells By Value
+lib/hyphy/ChartAddIns/Contigency Table
+lib/hyphy/ChartAddIns/Covariance
+lib/hyphy/ChartAddIns/DBAddIns/DescriptiveStats.bf
+lib/hyphy/ChartAddIns/DBAddIns/FromSQLFlatFile.bf
+lib/hyphy/ChartAddIns/DBAddIns/HY_DBW_TemplateList
+lib/hyphy/ChartAddIns/DBAddIns/ToChartWindow.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToConsole.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToFastaFile.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToSQLFlatFile.bf
+lib/hyphy/ChartAddIns/DBAddIns/ToTabFile.bf
+lib/hyphy/ChartAddIns/Descriptive Statistics
+lib/hyphy/ChartAddIns/Distribution Moments
+lib/hyphy/ChartAddIns/DistributionAddIns/Event Posteriors
+lib/hyphy/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf
+lib/hyphy/ChartAddIns/DistributionAddIns/Most Likely Class Assignment
+lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Distribution
+lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Moments
+lib/hyphy/ChartAddIns/DistributionAddIns/Prior Moments
+lib/hyphy/ChartAddIns/Gaussian Penalty Clustering
+lib/hyphy/ChartAddIns/Goodness of Fit
+lib/hyphy/ChartAddIns/Histogram
+lib/hyphy/ChartAddIns/K-Mean Clustering
+lib/hyphy/ChartAddIns/KH Resampler
+lib/hyphy/ChartAddIns/Linear Fit
+lib/hyphy/ChartAddIns/Mean Profile Plot
+lib/hyphy/ChartAddIns/Median Profile Plot
+lib/hyphy/ChartAddIns/Poisson Mixture Fit
+lib/hyphy/ChartAddIns/Populate Cells
+lib/hyphy/ChartAddIns/Profile Mean Clustering
+lib/hyphy/ChartAddIns/Running Sum
+lib/hyphy/ChartAddIns/Samplers/lhc.bf
+lib/hyphy/ChartAddIns/Samplers/sir.bf
+lib/hyphy/ChartAddIns/Samplers/srs.ibf
+lib/hyphy/ChartAddIns/Select Cells By Index
+lib/hyphy/ChartAddIns/Select Cells By Value
+lib/hyphy/ChartAddIns/SingleColumn
+lib/hyphy/ChartAddIns/Sort
+lib/hyphy/DatapanelAddIns/Character Plot
+lib/hyphy/DatapanelAddIns/Character Plot Two
+lib/hyphy/DatapanelAddIns/Compare Subsets
+lib/hyphy/DatapanelAddIns/Sequence Plot
+lib/hyphy/DatapanelAddIns/TBD/Character Plot By Sequence
+lib/hyphy/DatapanelAddIns/ibfs/char_colors.def
+lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
+lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
+lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
+lib/hyphy/GeneticCodes/Ciliate.cod
+lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
+lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
+lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
+lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
+lib/hyphy/GeneticCodes/Mold_mtDNA.cod
+lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
+lib/hyphy/GeneticCodes/Vertebratemtdna.cod
+lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
+lib/hyphy/SubstitutionClasses/AAEFV/Equal
+lib/hyphy/SubstitutionClasses/AAEFV/Estimated
+lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
+lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
+lib/hyphy/SubstitutionClasses/CodonEFV/Equal
+lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
+lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
+lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
+lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
+lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
+lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
+lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
+lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
+lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
+lib/hyphy/SubstitutionClasses/NucEFV/Equal
+lib/hyphy/SubstitutionClasses/NucEFV/Estimated
+lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
+lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
+lib/hyphy/SubstitutionClasses/aa.bf
+lib/hyphy/SubstitutionClasses/codon.bf
+lib/hyphy/SubstitutionClasses/dinuc.bf
+lib/hyphy/SubstitutionClasses/nuc.bf
+lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
+lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
+lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
+lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
+lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
+lib/hyphy/SubstitutionModels/Binary/F81.mdl
+lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
+lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
+lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
+lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
+lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
+lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
+lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
+lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
+lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
+lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
+lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
+lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
+lib/hyphy/TemplateBatchFiles/454.bf
+lib/hyphy/TemplateBatchFiles/AAModelComparison.bf
+lib/hyphy/TemplateBatchFiles/AddABias.ibf
+lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
+lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData2.bf
+lib/hyphy/TemplateBatchFiles/BGM.bf
+lib/hyphy/TemplateBatchFiles/BS2007.bf
+lib/hyphy/TemplateBatchFiles/BUSTED-SRV.bf
+lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
+lib/hyphy/TemplateBatchFiles/BranchClassDNDS.bf
+lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf
+lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
+lib/hyphy/TemplateBatchFiles/BranchSwap.bf
+lib/hyphy/TemplateBatchFiles/CleanGaps.bf
+lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf
+lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
+lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
+lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
+lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
+lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
+lib/hyphy/TemplateBatchFiles/CodonUsageBias.bf
+lib/hyphy/TemplateBatchFiles/CompareSelectivePressure.bf
+lib/hyphy/TemplateBatchFiles/CompareSelectivePressureIVL.bf
+lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
+lib/hyphy/TemplateBatchFiles/DatedTipsMolecularClock.bf
+lib/hyphy/TemplateBatchFiles/DirectionalREL.bf
+lib/hyphy/TemplateBatchFiles/DirectionalREL_MF.bf
+lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
+lib/hyphy/TemplateBatchFiles/DistanceMatrix_Splits.bf
+lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
+lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
+lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
+lib/hyphy/TemplateBatchFiles/Distances/JC69
+lib/hyphy/TemplateBatchFiles/Distances/K2P
+lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
+lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
+lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
+lib/hyphy/TemplateBatchFiles/Distances/PC
+lib/hyphy/TemplateBatchFiles/Distances/PC_MH
+lib/hyphy/TemplateBatchFiles/Distances/PC_RV
+lib/hyphy/TemplateBatchFiles/Distances/T3P
+lib/hyphy/TemplateBatchFiles/Distances/TN84
+lib/hyphy/TemplateBatchFiles/Distances/TN93
+lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
+lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
+lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
+lib/hyphy/TemplateBatchFiles/Distances/p_Distance
+lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
+lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
+lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
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+lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
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+lib/hyphy/TemplateBatchFiles/GADatedClock.ibf
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+lib/hyphy/TemplateBatchFiles/GADatedClockProcessorM.bf
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+lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
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+lib/hyphy/TemplateBatchFiles/GA_CHC_kernel.ibf
+lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
+lib/hyphy/TemplateBatchFiles/Gateaux.bf
+lib/hyphy/TemplateBatchFiles/Gateaux2.bf
+lib/hyphy/TemplateBatchFiles/GateauxMR.bf
+lib/hyphy/TemplateBatchFiles/KHTest.bf
+lib/hyphy/TemplateBatchFiles/Kernel_PCA.bf
+lib/hyphy/TemplateBatchFiles/Kernel_k_means.bf
+lib/hyphy/TemplateBatchFiles/Kernel_support.ibf
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+lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
+lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
+lib/hyphy/TemplateBatchFiles/LocalBranchSiteTest.bf
+lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
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+lib/hyphy/TemplateBatchFiles/MEME_mf.bf
+lib/hyphy/TemplateBatchFiles/MFPSreader.def
+lib/hyphy/TemplateBatchFiles/MFPositiveSelection.bf
+lib/hyphy/TemplateBatchFiles/MFPositiveSelectionPooled.bf
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+lib/hyphy/TemplateBatchFiles/MaxChi2.bf
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+lib/hyphy/TemplateBatchFiles/MergeSites.bf
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+lib/hyphy/TemplateBatchFiles/ModelSelectorBranch.bf
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