gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Oct 27 10:15:56 2022 -0500
Changeset:	8577ef641fa4ba749816c373503b6b990a672553

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

Log Message:
gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8577ef641fa4ba749816c373503b6b990a672553

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

diffstat:
 Makefile                       |  1 +
 gffread/DESCR                  |  2 ++
 gffread/Makefile               | 31 ++++++++++++++++++
 gffread/PLIST                  |  2 ++
 gffread/distinfo               |  9 ++++++
 gffread/patches/patch-Makefile | 72 ++++++++++++++++++++++++++++++++++++++++++
 6 files changed, 117 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 10eba4824f..efc2058f46 100644
--- a/Makefile
+++ b/Makefile
@@ -1122,6 +1122,7 @@ SUBDIR+=	gerris-snapshot
 SUBDIR+=	getdns
 SUBDIR+=	getdp
 SUBDIR+=	gf2x
+SUBDIR+=	gffread
 SUBDIR+=	gfa
 SUBDIR+=	gfan
 SUBDIR+=	gfeedline
diff --git a/gffread/DESCR b/gffread/DESCR
new file mode 100644
index 0000000000..def9446aac
--- /dev/null
+++ b/gffread/DESCR
@@ -0,0 +1,2 @@
+GFF/GTF utility providing format conversions, filtering, FASTA sequence
+extraction and more.
diff --git a/gffread/Makefile b/gffread/Makefile
new file mode 100644
index 0000000000..6919d7c07d
--- /dev/null
+++ b/gffread/Makefile
@@ -0,0 +1,31 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Oct 27 09:58:19 CDT 2022               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+DISTNAME=	gffread-0.12.7
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=gpertea/}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
+COMMENT=	GFF/GTF format conversions, filtering, FASTA extraction, etc
+LICENSE=	mit
+
+GITHUB_SUBMODULES=	gpertea gclib v0.12.7 gclib
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+INSTALL_TARGET=	install-strip
+
+INSTALLATION_DIRS=	bin
+
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/gffread/PLIST b/gffread/PLIST
new file mode 100644
index 0000000000..50dbcee023
--- /dev/null
+++ b/gffread/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/gffread
diff --git a/gffread/distinfo b/gffread/distinfo
new file mode 100644
index 0000000000..57688bc7d5
--- /dev/null
+++ b/gffread/distinfo
@@ -0,0 +1,9 @@
+$NetBSD$
+
+BLAKE2s (gffread-0.12.7.tar.gz) = 4f39c075ca17fe6813595dd7c8d1ff2ff829f76b3d5eed46e28c7cbdaca56255
+SHA512 (gffread-0.12.7.tar.gz) = 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b
+Size (gffread-0.12.7.tar.gz) = 403734 bytes
+BLAKE2s (gpertea-gclib-v0.12.7.tar.gz) = 68a41720355aac7d8b0602a66c558cfdabd93594a9079761ab5332f7adece277
+SHA512 (gpertea-gclib-v0.12.7.tar.gz) = 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90
+Size (gpertea-gclib-v0.12.7.tar.gz) = 259314 bytes
+SHA1 (patch-Makefile) = 02268a6336c4a5f7488b0fb64842714ab04d0ec9
diff --git a/gffread/patches/patch-Makefile b/gffread/patches/patch-Makefile
new file mode 100644
index 0000000000..c5603c65ff
--- /dev/null
+++ b/gffread/patches/patch-Makefile
@@ -0,0 +1,72 @@
+$NetBSD$
+
+# Portability and package-friendliness
+
+--- Makefile.orig	2021-07-23 14:21:36 UTC
++++ Makefile
+@@ -1,11 +1,11 @@
+-GCLDIR := $(if $(GCLDIR),$(GCLDIR),../gclib)
++GCLDIR := $(if $(GCLDIR),$(GCLDIR),gclib)
+ 
+ SEARCHDIRS := -I. -I${GCLDIR}
+ 
+ SYSTYPE :=     $(shell uname)
+ 
+ CXX   := $(if $(CXX),$(CXX),g++)
+-LINKER  := $(if $(LINKER),$(LINKER),g++)
++LINKER  := $(if $(LINKER),$(LINKER),${CXX})
+ 
+ LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
+ 
+@@ -15,7 +15,7 @@ BASEFLAGS  := -Wall -Wextra -std=c++11 ${SEARCHDIRS} -
+ 
+ GCCV8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
+ ifeq "$(GCCV8)" "1"
+- BASEFLAGS += -Wno-class-memaccess
++ # BASEFLAGS += -Wno-class-memaccess
+ endif
+ 
+ CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))
+@@ -33,7 +33,7 @@ else #debug builds
+     LDFLAGS += -pg
+   else
+     #CXXFLAGS += -g -O0 -DNDEBUG
+-    CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
++    #CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
+   endif
+   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
+      #use sanitizer in gcc 4.9+
+@@ -79,11 +79,8 @@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/
+  
+ .PHONY : all
+ 
+-all static release debug memcheck memdebug profile gprof prof: ../gclib gffread
++all static release debug memcheck memdebug profile gprof prof: ${GCLDIR} gffread
+ 
+-../gclib:
+-	git clone https://github.com/gpertea/gclib.git ../gclib
+-
+ $(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+ gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+ gff_utils.o : gff_utils.h $(GCLDIR)/gff.h
+@@ -97,9 +94,19 @@ gffread: $(OBJS) gffread.o
+ 
+ # target for removing all object files
+ 
+-.PHONY : clean
++.PHONY : clean install install-strip
++
+ clean:
+ 	@${RM} gffread gffread.o* gffread.exe $(OBJS)
+ 	@${RM} core.*
+ 
++INSTALL	?= install
++STRIP	?= strip
++PREFIX	?= /usr/local
++DESTDIR	?= .
+ 
++install:
++	${INSTALL} -c gffread ${DESTDIR}${PREFIX}/bin
++
++install-strip: install
++	${STRIP} ${DESTDIR}${PREFIX}/bin/gffread