CVS commit: pkgsrc/biology/gffread

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sun Nov  6 23:01:18 UTC 2022

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

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/gffread/DESCR \
    pkgsrc/biology/gffread/Makefile pkgsrc/biology/gffread/PLIST \
    pkgsrc/biology/gffread/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/gffread/patches/patch-Makefile

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

Added files:

Index: pkgsrc/biology/gffread/DESCR
diff -u /dev/null pkgsrc/biology/gffread/DESCR:1.1
--- /dev/null   Sun Nov  6 23:01:18 2022
+++ pkgsrc/biology/gffread/DESCR        Sun Nov  6 23:01:17 2022
@@ -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.
Index: pkgsrc/biology/gffread/Makefile
diff -u /dev/null pkgsrc/biology/gffread/Makefile:1.1
--- /dev/null   Sun Nov  6 23:01:18 2022
+++ pkgsrc/biology/gffread/Makefile     Sun Nov  6 23:01:17 2022
@@ -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"
Index: pkgsrc/biology/gffread/PLIST
diff -u /dev/null pkgsrc/biology/gffread/PLIST:1.1
--- /dev/null   Sun Nov  6 23:01:18 2022
+++ pkgsrc/biology/gffread/PLIST        Sun Nov  6 23:01:17 2022
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2022/11/06 23:01:17 bacon Exp $
+bin/gffread
Index: pkgsrc/biology/gffread/distinfo
diff -u /dev/null pkgsrc/biology/gffread/distinfo:1.1
--- /dev/null   Sun Nov  6 23:01:18 2022
+++ pkgsrc/biology/gffread/distinfo     Sun Nov  6 23:01:18 2022
@@ -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

Index: pkgsrc/biology/gffread/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/gffread/patches/patch-Makefile:1.1
--- /dev/null   Sun Nov  6 23:01:18 2022
+++ pkgsrc/biology/gffread/patches/patch-Makefile       Sun Nov  6 23:01:18 2022
@@ -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