Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 531769) +++ head/biology/Makefile (revision 531770) @@ -1,175 +1,176 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk + SUBDIR += gcta SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/gcta/Makefile =================================================================== --- head/biology/gcta/Makefile (nonexistent) +++ head/biology/gcta/Makefile (revision 531770) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= gcta +DISTVERSION= 1.26.0 +CATEGORIES= biology +MASTER_SITES= https://cnsgenomics.com/software/gcta/pre_gcta/ +DISTNAME= ${PORTNAME}_${PORTVERSION}_src + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Genome-wide Complex Trait Analysis + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/GNU_General_Public_License_v3.txt + +BUILD_DEPENDS= eigen>=3:math/eigen3 +LIB_DEPENDS+= libopenblas.so:math/openblas + +USES= compiler:openmp dos2unix gmake localbase zip + +CXXFLAGS+= -I${LOCALBASE}/include/eigen3 -fopenmp +LDFLAGS+= -lopenblas + +INSTALL_TARGET= install-strip +PLIST_FILES= bin/gcta + +.include + +.if ${CHOSEN_COMPILER_TYPE} == gcc && ${COMPILER_VERSION} <= 42 +USE_GCC= yes +.endif + +do-extract: + ${UNZIP_NATIVE_CMD} -d ${WRKSRC} ${DISTDIR}/${DISTFILES} + +.include Property changes on: head/biology/gcta/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/distinfo =================================================================== --- head/biology/gcta/distinfo (nonexistent) +++ head/biology/gcta/distinfo (revision 531770) @@ -0,0 +1,3 @@ +TIMESTAMP = 1489125670 +SHA256 (gcta_1.26.0_src.zip) = 554c48f421c93cbaf64b1c300ca507d8e7a56086b5c7d857227fbd4048f42acf +SIZE (gcta_1.26.0_src.zip) = 198045 Property changes on: head/biology/gcta/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/files/patch-Makefile =================================================================== --- head/biology/gcta/files/patch-Makefile (nonexistent) +++ head/biology/gcta/files/patch-Makefile (revision 531770) @@ -0,0 +1,59 @@ +--- Makefile.orig 2020-04-15 01:43:44 UTC ++++ Makefile +@@ -6,21 +6,27 @@ + # --------------------------------------------------------------------- + + # Directory of the target +-OUTPUT = gcta64 ++OUTPUT = gcta + + # Compiler +-CXX = g++ ++CXX ?= g++ + + # EIGEN library +-EIGEN_PATH = ../../../Lib/eigen ++EIGEN_PATH ?= ../../../Lib/eigen + + # Intel MKL library +-MKL_PATH = /opt/intel/mkl ++MKL_PATH ?= /opt/intel/mkl + + # Compiler flags +-CXXFLAGS = -w -O3 -m64 -static -fopenmp -I $(EIGEN_PATH) -DEIGEN_NO_DEBUG -I $(MKL_PATH)/include +-LIB += -static -lz -Wl,--start-group $(MKL_PATH)/lib/intel64/libmkl_intel_lp64.a $(MKL_PATH)/lib/intel64/libmkl_gnu_thread.a $(MKL_PATH)/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl ++CXXFLAGS ?= -w -O3 -m64 -static -fopenmp -I $(EIGEN_PATH) -DEIGEN_NO_DEBUG -I $(MKL_PATH)/include ++LDFLAGS += -lz -Wl,--start-group -lpthread -lm -ldl + ++MKDIR ?= mkdir ++DESTDIR ?= . ++PREFIX ?= /usr/local ++INSTALL ?= install ++STRIP ?= strip ++ + HDR += CommFunc.h \ + cdflib.h \ + dcdflib.h \ +@@ -58,7 +64,7 @@ OBJ = $(SRC:.cpp=.o) + all : $(OUTPUT) + + $(OUTPUT) : +- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) ++ $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LDFLAGS) + + $(OBJ) : $(HDR) + +@@ -69,6 +75,13 @@ $(OBJ) : $(HDR) + $(OUTPUT) : $(OBJ) + + FORCE: ++ ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c ${OUTPUT} ${DESTDIR}${PREFIX}/bin ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/${OUTPUT} + + clean: + rm -f *.o Property changes on: head/biology/gcta/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/files/patch-eigen__func.h =================================================================== --- head/biology/gcta/files/patch-eigen__func.h (nonexistent) +++ head/biology/gcta/files/patch-eigen__func.h (revision 531770) @@ -0,0 +1,15 @@ +--- eigen_func.h.orig 2016-06-22 03:11:01 UTC ++++ eigen_func.h +@@ -12,9 +12,9 @@ + #ifndef _EIGENFUNC_H + #define _EIGENFUNC_H + +-#ifndef EIGEN_USE_MKL_ALL +-#define EIGEN_USE_MKL_ALL +-#endif ++//#ifndef EIGEN_USE_MKL_ALL ++//#define EIGEN_USE_MKL_ALL ++//#endif + + #include "CommFunc.h" + #include "StatFunc.h" Property changes on: head/biology/gcta/files/patch-eigen__func.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/files/patch-gcta.h =================================================================== --- head/biology/gcta/files/patch-gcta.h (nonexistent) +++ head/biology/gcta/files/patch-gcta.h (revision 531770) @@ -0,0 +1,29 @@ +--- gcta.h.orig 2016-06-22 03:11:01 UTC ++++ gcta.h +@@ -17,9 +17,9 @@ + #define EIGEN_YES_I_KNOW_SPARSE_MODULE_IS_NOT_STABLE_YET + #endif + +-#ifndef EIGEN_USE_MKL_ALL +-#define EIGEN_USE_MKL_ALL +-#endif ++//#ifndef EIGEN_USE_MKL_ALL ++//#define EIGEN_USE_MKL_ALL ++//#endif + + #include "CommFunc.h" + #include "StrFunc.h" +@@ -36,8 +36,11 @@ + #include + #include + #include +-#include +-#include ++#include ++#include ++// Looks like openblas, cblas and lapacke are all that's needed ++//#include ++//#include + + using namespace Eigen; + using namespace std; Property changes on: head/biology/gcta/files/patch-gcta.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/files/patch-ld.cpp =================================================================== --- head/biology/gcta/files/patch-ld.cpp (nonexistent) +++ head/biology/gcta/files/patch-ld.cpp (revision 531770) @@ -0,0 +1,13 @@ +--- ld.cpp.orig 2020-04-15 12:56:27 UTC ++++ ld.cpp +@@ -1004,7 +1004,9 @@ void gcta::calcu_max_ld_rsq_blk(eigenVector &multi_rsq + } + + +- SelfAdjointEigenSolver pca(rsq_sub.array()); ++ // Fixed compile by removing .array(). Not sure about the validity ++ // of this change, but it seemed reasonable based on constructor docs. ++ SelfAdjointEigenSolver pca(rsq_sub); + + // debug + // ofstream tmp("tmp_R.txt"); Property changes on: head/biology/gcta/files/patch-ld.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/files/patch-mkl.cpp =================================================================== --- head/biology/gcta/files/patch-mkl.cpp (nonexistent) +++ head/biology/gcta/files/patch-mkl.cpp (revision 531770) @@ -0,0 +1,56 @@ +--- mkl.cpp.orig 2020-04-15 00:54:40 UTC ++++ mkl.cpp +@@ -357,7 +357,7 @@ bool gcta::comput_inverse_logdet_LDLT_mkl(eigenMatrix + // MKL's Cholesky decomposition + int info = 0, int_n = (int) n; + char uplo = 'L'; +- dpotrf(&uplo, &int_n, Vi_mkl, &int_n, &info); ++ dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info); + //spotrf( &uplo, &n, Vi_mkl, &n, &info ); + if (info < 0) throw ("Error: Cholesky decomposition failed. Invalid values found in the matrix.\n"); + else if (info > 0) return false; +@@ -369,7 +369,7 @@ bool gcta::comput_inverse_logdet_LDLT_mkl(eigenMatrix + } + + // Calcualte V inverse +- dpotri(&uplo, &int_n, Vi_mkl, &int_n, &info); ++ dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info); + //spotri( &uplo, &n, Vi_mkl, &n, &info ); + if (info < 0) throw ("Error: invalid values found in the varaince-covaraince (V) matrix.\n"); + else if (info > 0) return false; +@@ -405,7 +405,7 @@ bool gcta::comput_inverse_logdet_LU_mkl(eigenMatrix &V + int LWORK = N*N; + double *WORK = new double[n * n]; + int INFO; +- dgetrf(&N, &N, Vi_mkl, &N, IPIV, &INFO); ++ dgetrf_(&N, &N, Vi_mkl, &N, IPIV, &INFO); + if (INFO < 0) throw ("Error: LU decomposition failed. Invalid values found in the matrix.\n"); + else if (INFO > 0) { + delete[] Vi_mkl; +@@ -418,7 +418,7 @@ bool gcta::comput_inverse_logdet_LU_mkl(eigenMatrix &V + } + + // Calcualte V inverse +- dgetri(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); ++ dgetri_(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); + if (INFO < 0) throw ("Error: invalid values found in the varaince-covaraince (V) matrix.\n"); + else if (INFO > 0) return false; + else { +@@ -453,7 +453,7 @@ bool gcta::comput_inverse_logdet_LU_mkl_array(int n, f + int LWORK = N*N; + double *WORK = new double[n * n]; + int INFO; +- dgetrf(&N, &N, Vi_mkl, &N, IPIV, &INFO); ++ dgetrf_(&N, &N, Vi_mkl, &N, IPIV, &INFO); + if (INFO < 0) throw ("Error: LU decomposition failed. Invalid values found in the matrix.\n"); + else if (INFO > 0) { + delete[] Vi_mkl; +@@ -467,7 +467,7 @@ bool gcta::comput_inverse_logdet_LU_mkl_array(int n, f + } + + // Calcualte V inverse +- dgetri(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); ++ dgetri_(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); + if (INFO < 0) throw ("Error: invalid values found in the varaince-covaraince (V) matrix.\n"); + else if (INFO > 0) return (false); // Vi.diagonal()=Vi.diagonal().array()+Vi.diagonal().mean()*1e-3; + else { Property changes on: head/biology/gcta/files/patch-mkl.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/gcta/pkg-descr =================================================================== --- head/biology/gcta/pkg-descr (nonexistent) +++ head/biology/gcta/pkg-descr (revision 531770) @@ -0,0 +1,7 @@ +GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate +the proportion of phenotypic variance explained by genome- or chromosome-wide +SNPs for complex traits (the GREML method), and has subsequently extended for +many other analyses to better understand the genetic architecture of complex +traits. + +WWW: http://cnsgenomics.com/software/gcta/index.html Property changes on: head/biology/gcta/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property