svn commit: r501873 - in head/biology: . gemma gemma/files
Jason W. Bacon
jwb at FreeBSD.org
Fri May 17 14:45:22 UTC 2019
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 at 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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