[pkgsrc/trunk]: pkgsrc/biology/gffread biology/gffread: GFF/GTF format conver...

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/b93eda9fb49d
branches:  trunk
changeset: 387795:b93eda9fb49d
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sun Nov 06 23:01:17 2022 +0000

description:
biology/gffread: GFF/GTF format conversions, filtering, etc

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.  The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.

diffstat:

 biology/gffread/DESCR                  |   7 +++
 biology/gffread/Makefile               |  19 ++++++++
 biology/gffread/PLIST                  |   2 +
 biology/gffread/distinfo               |   9 ++++
 biology/gffread/patches/patch-Makefile |  73 ++++++++++++++++++++++++++++++++++
 5 files changed, 110 insertions(+), 0 deletions(-)

diffs (130 lines):

diff -r 2529dee61424 -r b93eda9fb49d biology/gffread/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gffread/DESCR     Sun Nov 06 23:01:17 2022 +0000
@@ -0,0 +1,7 @@
+GFF/GTF utility providing format conversions, filtering, FASTA sequence
+extraction and more.  The program gffread can be used to validate,
+filter, convert and perform various other operations on GFF files.
+Because the program shares the same GFF parser code with Cufflinks,
+Stringtie, and gffcompare, it could be used to verify that a GFF file
+from a certain annotation source is correctly "understood" by these
+programs.
diff -r 2529dee61424 -r b93eda9fb49d biology/gffread/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gffread/Makefile  Sun Nov 06 23:01:17 2022 +0000
@@ -0,0 +1,19 @@
+# $NetBSD: Makefile,v 1.1 2022/11/06 23:01:17 bacon Exp $
+
+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
+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
+
+.include "../../mk/bsd.pkg.mk"
diff -r 2529dee61424 -r b93eda9fb49d biology/gffread/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gffread/PLIST     Sun Nov 06 23:01:17 2022 +0000
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2022/11/06 23:01:17 bacon Exp $
+bin/gffread
diff -r 2529dee61424 -r b93eda9fb49d biology/gffread/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gffread/distinfo  Sun Nov 06 23:01:17 2022 +0000
@@ -0,0 +1,9 @@
+$NetBSD: distinfo,v 1.1 2022/11/06 23:01:18 bacon Exp $
+
+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) = 07e83c4b17715f31f0429671dba703a8b1d31118
diff -r 2529dee61424 -r b93eda9fb49d biology/gffread/patches/patch-Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gffread/patches/patch-Makefile    Sun Nov 06 23:01:17 2022 +0000
@@ -0,0 +1,73 @@
+$NetBSD: patch-Makefile,v 1.1 2022/11/06 23:01:18 bacon Exp $
+
+# Portability and package-friendliness
+
+--- Makefile.orig      2021-07-23 14:21:36.000000000 +0000
++++ 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 $
+ 
+ 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+
+@@ -79,10 +79,7 @@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArg
+  
+ .PHONY : all
+ 
+-all static release debug memcheck memdebug profile gprof prof: ../gclib gffread
+-
+-../gclib:
+-      git clone https://github.com/gpertea/gclib.git ../gclib
++all static release debug memcheck memdebug profile gprof prof: ${GCLDIR} gffread
+ 
+ $(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+ gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+@@ -97,9 +94,21 @@ 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.*
+ 
++MKDIR ?= mkdir
++INSTALL       ?= install
++STRIP ?= strip
++PREFIX        ?= /usr/local
++DESTDIR       ?= .
++
++install:
++      ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
++      ${INSTALL} -c gffread ${DESTDIR}${PREFIX}/bin
+ 
++install-strip: install
++      ${STRIP} ${DESTDIR}${PREFIX}/bin/gffread