Date: Fri, 17 May 2019 14:45:20 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r501873 - in head/biology: . gemma gemma/files Message-ID: <201905171445.x4HEjKE4084764@repo.freebsd.org>
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Author: jwb Date: Fri May 17 14:45:19 2019 New Revision: 501873 URL: https://svnweb.freebsd.org/changeset/ports/501873 Log: biology/gemma: Genome-wide Efficient Mixed Model Association 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. Added: head/biology/gemma/ head/biology/gemma/Makefile (contents, props changed) head/biology/gemma/distinfo (contents, props changed) head/biology/gemma/files/ head/biology/gemma/files/Makefile (contents, props changed) head/biology/gemma/files/patch-doc_manual.tex (contents, props changed) head/biology/gemma/files/patch-src_gemma.cpp (contents, props changed) head/biology/gemma/pkg-descr (contents, props changed) head/biology/gemma/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri May 17 14:16:30 2019 (r501872) +++ head/biology/Makefile Fri May 17 14:45:19 2019 (r501873) @@ -42,6 +42,7 @@ SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk + SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic Added: head/biology/gemma/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/Makefile Fri May 17 14:45:19 2019 (r501873) @@ -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 <bsd.port.pre.mk> + +# 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 <bsd.port.post.mk> Added: head/biology/gemma/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/distinfo Fri May 17 14:45:19 2019 (r501873) @@ -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 Added: head/biology/gemma/files/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/files/Makefile Fri May 17 14:45:19 2019 (r501873) @@ -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 Added: head/biology/gemma/files/patch-doc_manual.tex ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/files/patch-doc_manual.tex Fri May 17 14:45:19 2019 (r501873) @@ -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 Added: head/biology/gemma/files/patch-src_gemma.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/files/patch-src_gemma.cpp Fri May 17 14:45:19 2019 (r501873) @@ -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; + } Added: head/biology/gemma/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/pkg-descr Fri May 17 14:45:19 2019 (r501873) @@ -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 Added: head/biology/gemma/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gemma/pkg-plist Fri May 17 14:45:19 2019 (r501873) @@ -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
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