GenericRepeatFinder: import GenericRepeatFinder-1.0 as wip/GenericRepeatFinder.

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Wed Jun 8 10:41:45 2022 -0600
Changeset:	6589577601daf30236a9ef934c85a959e800b764

Modified Files:
	Makefile
Added Files:
	GenericRepeatFinder/DESCR
	GenericRepeatFinder/Makefile
	GenericRepeatFinder/PLIST
	GenericRepeatFinder/distinfo
	GenericRepeatFinder/patches/patch-src_Makefile

Log Message:
GenericRepeatFinder: import GenericRepeatFinder-1.0 as wip/GenericRepeatFinder.

Generic Repeat Finder (GRF) is a C++ program package for detecting
terminal inverted repeats (TIRs), terminal direct repeats (TDRs),
interspersed repeats, miniature inverted repeat transposable elements
(MITEs), and long terminal repeat (LTR) transposons in genomes.

If you have any question or comment, please contact Dr. Chun Liang
(liangc%miamioh.edu@localhost).

This software is an open-source tool that follows specifications from
the website (http://creativecommons.org/licenses/by-nc-sa/3.0/).

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6589577601daf30236a9ef934c85a959e800b764

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 GenericRepeatFinder/DESCR                      |  4 ++
 GenericRepeatFinder/Makefile                   | 52 ++++++++++++++++++++++++++
 GenericRepeatFinder/PLIST                      | 12 ++++++
 GenericRepeatFinder/distinfo                   |  6 +++
 GenericRepeatFinder/patches/patch-src_Makefile | 14 +++++++
 Makefile                                       |  1 +
 6 files changed, 89 insertions(+)

diffs:
diff --git a/GenericRepeatFinder/DESCR b/GenericRepeatFinder/DESCR
new file mode 100644
index 0000000000..f72778c095
--- /dev/null
+++ b/GenericRepeatFinder/DESCR
@@ -0,0 +1,4 @@
+Generic Repeat Finder (GRF) is a C++ program package for detecting
+terminal inverted repeats (TIRs), terminal direct repeats (TDRs),
+interspersed repeats, miniature inverted repeat transposable elements
+(MITEs), and long terminal repeat (LTR) transposons in genomes.
diff --git a/GenericRepeatFinder/Makefile b/GenericRepeatFinder/Makefile
new file mode 100644
index 0000000000..57022c2318
--- /dev/null
+++ b/GenericRepeatFinder/Makefile
@@ -0,0 +1,52 @@
+# $NetBSD$
+
+DISTNAME=	GenericRepeatFinder-1.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=bioinfolabmu/}
+GITHUB_TAG=	refs/tags/v${PKGVERSION_NOREV}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/bioinfolabmu/GenericRepeatFinder/
+COMMENT=	Detect repeated sequences in genomes
+LICENSE=	gnu-gpl-v3
+
+WRKSRC=		${WRKDIR}/${DISTNAME}
+BUILD_DIRS+=	src
+USE_LANGUAGES=	c c++
+MAKE_ENV+=	OPENMP_CFLAGS=${OPENMP_CFLAGS:Q}
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == "Darwin"
+# see https://mac.r-project.org/openmp/
+OPENMP_CFLAGS=	-Xclang -fopenmp
+LIBS+=		-lomp
+.else
+OPENMP_CFLAGS=	-fopenmp
+.endif
+
+INSTALLATION_DIRS+=	bin share/doc/GenericRepeatFinder
+
+BIN_FILES+=	grf-alignment
+BIN_FILES+=	grf-alignment2
+BIN_FILES+=	grf-dbn
+BIN_FILES+=	grf-filter
+BIN_FILES+=	grf-intersperse
+BIN_FILES+=	grf-main
+BIN_FILES+=	grf-mite-cluster
+BIN_FILES+=	grf-nest
+BIN_FILES+=	ltr_finder
+
+DOC_FILES+=	QuickGuideForReviewer.txt
+DOC_FILES+=	readme.txt
+
+do-install:
+.for f in ${BIN_FILES}
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/${f} ${DESTDIR}${PREFIX}/bin/${f}
+.endfor
+.for f in ${DOC_FILES}
+	${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/doc/GenericRepeatFinder/${f}
+.endfor
+
+.include "../../parallel/openmp/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/GenericRepeatFinder/PLIST b/GenericRepeatFinder/PLIST
new file mode 100644
index 0000000000..91fe867724
--- /dev/null
+++ b/GenericRepeatFinder/PLIST
@@ -0,0 +1,12 @@
+@comment $NetBSD$
+bin/grf-alignment
+bin/grf-alignment2
+bin/grf-dbn
+bin/grf-filter
+bin/grf-intersperse
+bin/grf-main
+bin/grf-mite-cluster
+bin/grf-nest
+bin/ltr_finder
+share/doc/GenericRepeatFinder/QuickGuideForReviewer.txt
+share/doc/GenericRepeatFinder/readme.txt
diff --git a/GenericRepeatFinder/distinfo b/GenericRepeatFinder/distinfo
new file mode 100644
index 0000000000..72e1d000f7
--- /dev/null
+++ b/GenericRepeatFinder/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+BLAKE2s (GenericRepeatFinder-1.0.tar.gz) = b2c7bb02748cf71d93a79aab2e79e5fd575fe7c2393002732e0010b4b96516e3
+SHA512 (GenericRepeatFinder-1.0.tar.gz) = 228ec68ee724fe97584690e9c13433659d28575e4dbbba7d22847312f4e53d1043cec7d9d8d5b98ebf23464fa4b0ce65392f02bb9c82b6a4427b27aa41e8b27b
+Size (GenericRepeatFinder-1.0.tar.gz) = 4327498 bytes
+SHA1 (patch-src_Makefile) = a8caa0ca08cf836f754426cce4837958dbcf6f00
diff --git a/GenericRepeatFinder/patches/patch-src_Makefile b/GenericRepeatFinder/patches/patch-src_Makefile
new file mode 100644
index 0000000000..eb681c1ad8
--- /dev/null
+++ b/GenericRepeatFinder/patches/patch-src_Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+Handle OpenMP on Darwin, where native clang does not support -fopenmp.
+See https://mac.r-project.org/openmp/.
+
+--- src/Makefile.orig	2019-05-19 02:52:11.000000000 +0000
++++ src/Makefile
+@@ -1,5 +1,5 @@
+ # Define required macros here
+-CFLAGS = -Wall -std=c++11 -O3 -fopenmp
++CFLAGS = -Wall -std=c++11 -O3 ${OPENMP_CFLAGS}
+ CC = g++
+ INCLUDES = -Igrf-main -Igrf-intersperse -Igrf-mite-cluster
+ 
diff --git a/Makefile b/Makefile
index 694bc977c3..6910b57347 100644
--- a/Makefile
+++ b/Makefile
@@ -16,6 +16,7 @@ SUBDIR+=	CuraEngine
 SUBDIR+=	ETL
 SUBDIR+=	FLIF
 SUBDIR+=	FLIF-git
+SUBDIR+=	GenericRepeatFinder
 SUBDIR+=	GNUMail-pgp
 SUBDIR+=	GSAlign
 SUBDIR+=	GSCommander