Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 501872) +++ head/biology/Makefile (revision 501873) @@ -1,164 +1,165 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed 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 += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm 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 += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac 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-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-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-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent 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 += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/gemma/Makefile =================================================================== --- head/biology/gemma/Makefile (nonexistent) +++ head/biology/gemma/Makefile (revision 501873) @@ -0,0 +1,44 @@ +# $FreeBSD$ + +PORTNAME= GEMMA +DISTVERSION= 0.98.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Genome-wide Efficient Mixed Model Association + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libcblas.so:math/cblas \ + libgsl.so:math/gsl + +USES= blaslapack:openblas compiler:c++11-lang eigen:3 gmake \ + localbase:ldflags +USE_GITHUB= yes +GH_ACCOUNT= genetics-statistics + +MAKEFILE= ${FILESDIR}/Makefile +CXXFLAGS+= -I${LOCALBASE}/include/eigen3 -DOPENBLAS -DOPENBLAS_LEGACY +LDFLAGS+= -lopenblas + +OPTIONS_DEFINE= EXAMPLES + +.include + +# Force newer GCC on platforms using GCC 4.2 as base +.if ${CHOSEN_COMPILER_TYPE} == gcc +USE_GCC= yes +.endif + +pre-configure: + @${REINPLACE_CMD} -e 's|../bin/gemma|../gemma|' ${WRKSRC}/test/*.sh + +do-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) + +do-test: + (cd ${WRKSRC}/test && ${SH} test_suite.sh) + +.include Property changes on: head/biology/gemma/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/gemma/distinfo =================================================================== --- head/biology/gemma/distinfo (nonexistent) +++ head/biology/gemma/distinfo (revision 501873) @@ -0,0 +1,3 @@ +TIMESTAMP = 1558018021 +SHA256 (genetics-statistics-GEMMA-0.98.1_GH0.tar.gz) = 6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b +SIZE (genetics-statistics-GEMMA-0.98.1_GH0.tar.gz) = 49569015 Property changes on: head/biology/gemma/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/gemma/files/Makefile =================================================================== --- head/biology/gemma/files/Makefile (nonexistent) +++ head/biology/gemma/files/Makefile (revision 501873) @@ -0,0 +1,68 @@ + +GEMMA_VERSION = $(shell cat ./VERSION) +VGEN = scripts/gen_version_info.sh +CXXFLAGS += -DHAVE_INLINE -pthread -Wall -std=gnu++11 +CXXFLAGS += -DNDEBUG -Icontrib/catch-1.9.7 -Isrc + +SRC_DIR = ./src +TEST_SRC_DIR = ./test/src +DESTDIR ?= . +PREFIX ?= /usr/local +MKDIR ?= mkdir +INSTALL ?= install + +BIN = gemma +HDR = $(wildcard src/*.h) ./src/version.h +SOURCES = $(wildcard src/*.cpp) +OBJS = $(SOURCES:.cpp=.o) +LDFLAGS += -lgsl -lz + +.PHONY: all test + +all: $(BIN) + +./src/version.h: ./VERSION + $(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h) + +$(BIN): $(OBJS) + $(CXX) $(CXXFLAGS) -o $(BIN) $(OBJS) $(LDFLAGS) + +$(OBJS): $(HDR) + +install: all + $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin + $(INSTALL) -s -c $(BIN) $(DESTDIR)$(PREFIX)/bin + +.SUFFIXES : .cpp .c .o $(SUFFIXES) + +./bin/unittests-gemma: contrib/catch-1.9.7/catch.hpp $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS) + $(CXX) $(CXXFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma + +unittests: all ./bin/unittests-gemma + ./bin/unittests-gemma + +fast-check: all unittests + rm -vf test/output/* + cd test && ./dev_test_suite.sh | tee ../dev_test.log + grep -q 'success rate: 100%' dev_test.log + +slow-check: all + rm -vf test/output/* + cd test && ./test_suite.sh | tee ../test.log + grep -q 'success rate: 100%' test.log + +lengthy-check: all + rm -vf test/output/* + cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log + grep -q 'success rate: 100%' lengthy_test.log + +check: fast-check slow-check + +check-all: check lengthy-check + +clean: + rm -vf $(SRC_DIR)/*.o + rm -vf $(SRC_DIR)/*~ + rm -vf $(TEST_SRC_DIR)/*.o + rm -vf $(BIN) + rm -vf ./bin/unittests-gemma Property changes on: head/biology/gemma/files/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/gemma/files/patch-doc_manual.tex =================================================================== --- head/biology/gemma/files/patch-doc_manual.tex (nonexistent) +++ head/biology/gemma/files/patch-doc_manual.tex (revision 501873) @@ -0,0 +1,124 @@ +--- doc/manual.tex.orig 2019-04-18 21:03:11 UTC ++++ doc/manual.tex +@@ -767,8 +767,8 @@ of ``nan"s. + The basic usages for linear model association analysis with either the PLINK binary ped format or the BIMBAM format are: + + \begin{verbatim} +-./gemma -bfile [prefix] -lm [num] -o [prefix] +-./gemma -g [filename] -p [filename] -a [filename] -lm [num] -o [prefix] ++gemma -bfile [prefix] -lm [num] -o [prefix] ++gemma -g [filename] -p [filename] -a [filename] -lm [num] -o [prefix] + \end{verbatim} + + where the ``-lm [num]" option specifies which frequentist test to use, +@@ -825,8 +825,8 @@ The basic usages to calculate an estimated relatedness + either the PLINK binary ped format or the BIMBAM format are: + % + \begin{verbatim} +-./gemma -bfile [prefix] -gk [num] -o [prefix] +-./gemma -g [filename] -p [filename] -gk [num] -o [prefix] ++gemma -bfile [prefix] -gk [num] -o [prefix] ++gemma -g [filename] -p [filename] -gk [num] -o [prefix] + \end{verbatim} + % + where the ``-gk [num]" option specifies which relatedness matrix to +@@ -887,8 +887,8 @@ matrix with either the PLINK binary ped format or the + are: + % + \begin{verbatim} +-./gemma -bfile [prefix] -k [filename] -eigen -o [prefix] +-./gemma -g [filename] -p [filename] -k [filename] -eigen -o [prefix] ++gemma -bfile [prefix] -k [filename] -eigen -o [prefix] ++gemma -g [filename] -p [filename] -k [filename] -eigen -o [prefix] + \end{verbatim} + % + where the ``-bfile [prefix]" specifies PLINK binary ped file prefix; +@@ -923,8 +923,8 @@ The basic usages for association analysis with either + ped format or the BIMBAM format are: + + \begin{verbatim} +-./gemma -bfile [prefix] -k [filename] -lmm [num] -o [prefix] +-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] -o [prefix] ++gemma -bfile [prefix] -k [filename] -lmm [num] -o [prefix] ++gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] -o [prefix] + \end{verbatim} + + where the ``-lmm [num]" option specifies which frequentist test to +@@ -1037,8 +1037,8 @@ The basic usages for association analysis with either + ped format or the BIMBAM format are: + + \begin{verbatim} +-./gemma -bfile [prefix] -k [filename] -lmm [num] -n [num1] [num2] [num3] -o [prefix] +-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] ++gemma -bfile [prefix] -k [filename] -lmm [num] -n [num1] [num2] [num3] -o [prefix] ++gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] + -n [num1] [num2] [num3] -o [prefix] + \end{verbatim} + +@@ -1069,8 +1069,8 @@ In addition, when a small proportion of phenotypes are + missing, one can impute these missing values before association tests: + + \begin{verbatim} +-./gemma -bfile [prefix] -k [filename] -predict -n [num1] [num2] [num3] -o [prefix] +-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict ++gemma -bfile [prefix] -k [filename] -predict -n [num1] [num2] [num3] -o [prefix] ++gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict + -n [num1] [num2] [num3] -o [prefix] + \end{verbatim} + +@@ -1099,8 +1099,8 @@ The basic usages for fitting a BSLMM with either the P + format or the BIMBAM format are: + + \begin{verbatim} +-./gemma -bfile [prefix] -bslmm [num] -o [prefix] +-./gemma -g [filename] -p [filename] -a [filename] -bslmm [num] -o [prefix] ++gemma -bfile [prefix] -bslmm [num] -o [prefix] ++gemma -g [filename] -p [filename] -a [filename] -bslmm [num] -o [prefix] + \end{verbatim} + + where the ``-bslmm [num]" option specifies which model to fit, +@@ -1225,9 +1225,9 @@ The basic usages for association analysis with either + ped format or the BIMBAM format are: + + \begin{verbatim} +-./gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename] ++gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename] + -predict [num] -o [prefix] +-./gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename] ++gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename] + -k [filename] -predict [num] -o [prefix] + \end{verbatim} + +@@ -1300,8 +1300,8 @@ The basic usages for variance component estimation wit + matrices are: + + \begin{verbatim} +-./gemma -p [filename] -k [filename] -n [num] -vc [num] -o [prefix] +-./gemma -p [filename] -mk [filename] -n [num] -vc [num] -o [prefix] ++gemma -p [filename] -k [filename] -n [num] -vc [num] -o [prefix] ++gemma -p [filename] -mk [filename] -n [num] -vc [num] -o [prefix] + \end{verbatim} + + where the ``-vc [num]" option specifies which estimation to use, in +@@ -1349,8 +1349,8 @@ binary ped format or the BIMBAM format. The basic usag + component estimation with summary statistics are: + + \begin{verbatim} +-./gemma -beta [filename] -bfile [prefix] -vc 1 -o [prefix] +-./gemma -beta [filename] -g [filename] -p [filename] -a [filename] -vc 1 -o [prefix] ++gemma -beta [filename] -bfile [prefix] -vc 1 -o [prefix] ++gemma -beta [filename] -g [filename] -p [filename] -a [filename] -vc 1 -o [prefix] + \end{verbatim} + + where the ``-vc 1" option specifies to use MQS-HEW; ``-beta +@@ -1395,8 +1395,8 @@ previous MQS run. The basic usages for using the asymp + compute the confidence intervals are + + \begin{verbatim} +-./gemma -beta [filename] -bfile [prefix] -ref [prefix] -pve [num] -ci 1 -o [prefix] +-./gemma -beta [filename] -g [filename] -p [filename] -ref [prefix] -pve [num] -ci 1 -o [prefix] ++gemma -beta [filename] -bfile [prefix] -ref [prefix] -pve [num] -ci 1 -o [prefix] ++gemma -beta [filename] -g [filename] -p [filename] -ref [prefix] -pve [num] -ci 1 -o [prefix] + \end{verbatim} + + In the above usages, ``-ref [prefix]" specifies the prefix of the Property changes on: head/biology/gemma/files/patch-doc_manual.tex ___________________________________________________________________ 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/gemma/files/patch-src_gemma.cpp =================================================================== --- head/biology/gemma/files/patch-src_gemma.cpp (nonexistent) +++ head/biology/gemma/files/patch-src_gemma.cpp (revision 501873) @@ -0,0 +1,166 @@ +--- src/gemma.cpp.orig 2019-04-18 21:03:48 UTC ++++ src/gemma.cpp +@@ -154,7 +154,7 @@ void GEMMA::PrintHelp(size_t option) { + + if (option == 0) { + cout << endl; +- cout << " type ./gemma -h [num] for detailed help" << endl; ++ cout << " type gemma -h [num] for detailed help" << endl; + cout << " options: " << endl; + cout << " 1: quick guide" << endl; + cout << " 2: file I/O related" << endl; +@@ -176,116 +176,116 @@ void GEMMA::PrintHelp(size_t option) { + if (option == 1) { + cout << " QUICK GUIDE" << endl; + cout << " to generate a relatedness matrix: " << endl; +- cout << " ./gemma -bfile [prefix] -gk [num] -o [prefix]" << endl; +- cout << " ./gemma -g [filename] -p [filename] -gk [num] -o [prefix]" ++ cout << " gemma -bfile [prefix] -gk [num] -o [prefix]" << endl; ++ cout << " gemma -g [filename] -p [filename] -gk [num] -o [prefix]" + << endl; + cout << " to generate the S matrix: " << endl; +- cout << " ./gemma -bfile [prefix] -gs -o [prefix]" << endl; +- cout << " ./gemma -p [filename] -g [filename] -gs -o [prefix]" ++ cout << " gemma -bfile [prefix] -gs -o [prefix]" << endl; ++ cout << " gemma -p [filename] -g [filename] -gs -o [prefix]" + << endl; +- cout << " ./gemma -bfile [prefix] -cat [filename] -gs -o [prefix]" ++ cout << " gemma -bfile [prefix] -cat [filename] -gs -o [prefix]" + << endl; +- cout << " ./gemma -p [filename] -g [filename] -cat [filename] -gs " ++ cout << " gemma -p [filename] -g [filename] -cat [filename] -gs " + "-o [prefix]" + << endl; +- cout << " ./gemma -bfile [prefix] -sample [num] -gs -o [prefix]" ++ cout << " gemma -bfile [prefix] -sample [num] -gs -o [prefix]" + << endl; +- cout << " ./gemma -p [filename] -g [filename] -sample [num] -gs -o " ++ cout << " gemma -p [filename] -g [filename] -sample [num] -gs -o " + "[prefix]" + << endl; + cout << " to generate the q vector: " << endl; +- cout << " ./gemma -beta [filename] -gq -o [prefix]" << endl; +- cout << " ./gemma -beta [filename] -cat [filename] -gq -o [prefix]" ++ cout << " gemma -beta [filename] -gq -o [prefix]" << endl; ++ cout << " gemma -beta [filename] -cat [filename] -gq -o [prefix]" + << endl; + cout << " to generate the ldsc weigthts: " << endl; +- cout << " ./gemma -beta [filename] -gw -o [prefix]" << endl; +- cout << " ./gemma -beta [filename] -cat [filename] -gw -o [prefix]" ++ cout << " gemma -beta [filename] -gw -o [prefix]" << endl; ++ cout << " gemma -beta [filename] -cat [filename] -gw -o [prefix]" + << endl; + cout << " to perform eigen decomposition of the relatedness matrix: " + << endl; +- cout << " ./gemma -bfile [prefix] -k [filename] -eigen -o [prefix]" ++ cout << " gemma -bfile [prefix] -k [filename] -eigen -o [prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -k [filename] -eigen " ++ cout << " gemma -g [filename] -p [filename] -k [filename] -eigen " + "-o [prefix]" + << endl; + cout << " to estimate variance components: " << endl; +- cout << " ./gemma -bfile [prefix] -k [filename] -vc [num] -o " ++ cout << " gemma -bfile [prefix] -k [filename] -vc [num] -o " + "[prefix]" + << endl; +- cout << " ./gemma -p [filename] -k [filename] -vc [num] -o [prefix]" ++ cout << " gemma -p [filename] -k [filename] -vc [num] -o [prefix]" + << endl; +- cout << " ./gemma -bfile [prefix] -mk [filename] -vc [num] -o " ++ cout << " gemma -bfile [prefix] -mk [filename] -vc [num] -o " + "[prefix]" + << endl; + cout +- << " ./gemma -p [filename] -mk [filename] -vc [num] -o [prefix]" +- << endl; +- cout << " ./gemma -beta [filename] -cor [filename] -vc [num] -o " ++ << " gemma -p [filename] -mk [filename] -vc [num] -o [prefix]" ++ << endl; ++ cout << " gemma -beta [filename] -cor [filename] -vc [num] -o " + "[prefix]" + << endl; +- cout << " ./gemma -beta [filename] -cor [filename] -cat [filename] " ++ cout << " gemma -beta [filename] -cor [filename] -cat [filename] " + "-vc [num] -o [prefix]" + << endl; + cout << " options for the above two commands: -crt -windowbp [num]" + << endl; +- cout << " ./gemma -mq [filename] -ms [filename] -mv [filename] -vc " ++ cout << " gemma -mq [filename] -ms [filename] -mv [filename] -vc " + "[num] -o [prefix]" + << endl; + cout << " or with summary statistics, replace bfile with mbfile, " + "or g or mg; vc=1 for HE weights and vc=2 for LDSC weights" + << endl; +- cout << " ./gemma -beta [filename] -bfile [filename] -cat " ++ cout << " gemma -beta [filename] -bfile [filename] -cat " + "[filename] -wsnp [filename] -wcat [filename] -vc [num] -o [prefix]" + << endl; +- cout << " ./gemma -beta [filename] -bfile [filename] -cat " ++ cout << " gemma -beta [filename] -bfile [filename] -cat " + "[filename] -wsnp [filename] -wcat [filename] -ci [num] -o [prefix]" + << endl; + cout << " to fit a linear mixed model: " << endl; +- cout << " ./gemma -bfile [prefix] -k [filename] -lmm [num] -o " ++ cout << " gemma -bfile [prefix] -k [filename] -lmm [num] -o " + "[prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -a [filename] -k " ++ cout << " gemma -g [filename] -p [filename] -a [filename] -k " + "[filename] -lmm [num] -o [prefix]" + << endl; + cout << " to fit a linear mixed model to test g by e effects: " << endl; +- cout << " ./gemma -bfile [prefix] -gxe [filename] -k [filename] " ++ cout << " gemma -bfile [prefix] -gxe [filename] -k [filename] " + "-lmm [num] -o [prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -a [filename] -gxe " ++ cout << " gemma -g [filename] -p [filename] -a [filename] -gxe " + "[filename] -k [filename] -lmm [num] -o [prefix]" + << endl; + cout << " to fit a univariate linear mixed model with different residual " + "weights for different individuals: " + << endl; +- cout << " ./gemma -bfile [prefix] -weight [filename] -k [filename] " ++ cout << " gemma -bfile [prefix] -weight [filename] -k [filename] " + "-lmm [num] -o [prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -a [filename] " ++ cout << " gemma -g [filename] -p [filename] -a [filename] " + "-weight [filename] -k [filename] -lmm [num] -o [prefix]" + << endl; + cout << " to fit a multivariate linear mixed model: " << endl; +- cout << " ./gemma -bfile [prefix] -k [filename] -lmm [num] -n " ++ cout << " gemma -bfile [prefix] -k [filename] -lmm [num] -n " + "[pheno cols...] -o [prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -a [filename] -k " ++ cout << " gemma -g [filename] -p [filename] -a [filename] -k " + "[filename] -lmm [num] -n [pheno cols...] -o [prefix]" + << endl; + cout << " to fit a Bayesian sparse linear mixed model: " << endl; +- cout << " ./gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl; +- cout << " ./gemma -g [filename] -p [filename] -a [filename] -bslmm " ++ cout << " gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl; ++ cout << " gemma -g [filename] -p [filename] -a [filename] -bslmm " + "[num] -o [prefix]" + << endl; + cout << " to obtain predicted values: " << endl; +- cout << " ./gemma -bfile [prefix] -epm [filename] -emu [filename] " ++ cout << " gemma -bfile [prefix] -epm [filename] -emu [filename] " + "-ebv [filename] -k [filename] -predict [num] -o [prefix]" + << endl; +- cout << " ./gemma -g [filename] -p [filename] -epm [filename] -emu " ++ cout << " gemma -g [filename] -p [filename] -epm [filename] -emu " + "[filename] -ebv [filename] -k [filename] -predict [num] -o " + "[prefix]" + << endl; + cout << " to calculate correlations between SNPs: " << endl; +- cout << " ./gemma -bfile [prefix] -calccor -o [prefix]" << endl; +- cout << " ./gemma -g [filename] -p [filename] -calccor -o [prefix]" ++ cout << " gemma -bfile [prefix] -calccor -o [prefix]" << endl; ++ cout << " gemma -g [filename] -p [filename] -calccor -o [prefix]" + << endl; + cout << endl; + } Property changes on: head/biology/gemma/files/patch-src_gemma.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/gemma/pkg-descr =================================================================== --- head/biology/gemma/pkg-descr (nonexistent) +++ head/biology/gemma/pkg-descr (revision 501873) @@ -0,0 +1,5 @@ +GEMMA is a software toolkit for fast application of linear mixed models (LMMs) +and related models to genome-wide association studies (GWAS) and other +large-scale data sets. + +WWW: https://github.com/genetics-statistics/GEMMA Property changes on: head/biology/gemma/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 Index: head/biology/gemma/pkg-plist =================================================================== --- head/biology/gemma/pkg-plist (nonexistent) +++ head/biology/gemma/pkg-plist (revision 501873) @@ -0,0 +1,20 @@ +bin/gemma +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_covariates.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_covariates2.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_geno.txt.gz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_pheno.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_snps.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.bed +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.bim +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.fam +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.simu.pheno.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC_covariates.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/demo.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.anno.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.bed +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.bim +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.fam +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.geno.txt.gz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.pheno.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940_snps.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940_snps_anno.txt Property changes on: head/biology/gemma/pkg-plist ___________________________________________________________________ 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