commit: b71c9dc45d0a26f46930158e146103fd8287260c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 07:41:48 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 07:41:48 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b71c9dc4
sci-biology/gffcompare: new package
Is a mixture of gclib object and gffcompare objects, hence
the download of two tar.gz files.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/gffcompare/files/Makefile.patch | 79 +++++++++++++++++++++++++
sci-biology/gffcompare/gffcompare-0.10.5.ebuild | 31 ++++++++++
sci-biology/gffcompare/metadata.xml | 12 ++++
3 files changed, 122 insertions(+)
diff --git a/sci-biology/gffcompare/files/Makefile.patch
b/sci-biology/gffcompare/files/Makefile.patch
new file mode 100644
index 000000000..afb52b2e1
--- /dev/null
+++ b/sci-biology/gffcompare/files/Makefile.patch
@@ -0,0 +1,79 @@
+--- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200
++++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200
+@@ -16,7 +16,7 @@
+ endif
+
+ # CVS checked in
+-CC := g++
++CXX ?= g++
+ BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \
+ -fno-exceptions -fno-rtti -D_REENTRANT
+
+@@ -24,7 +24,8 @@
+
+ ifneq (,$(filter %release %static, $(MAKECMDGOALS)))
+ # -- release build
+- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS)
++ CXXFLAGS ?= -O3 -g
++ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
+ LDFLAGS =
+ LIBS =
+ ifneq (,$(findstring static,$(MAKECMDGOALS)))
+@@ -37,16 +38,16 @@
+ ifeq "$(GCCVER49)" "0"
+ $(error gcc version 4.9 or greater is required for this build target)
+ endif
+- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address
++ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined
-fsanitize=address
+ GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5)
+ ifeq "$(GCCVER5)" "1"
+- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
+- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
+- #CFLAGS += -fcheck-pointer-bounds -mmpx
++ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero
-fsanitize=vptr
++ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size
++ #CXXFLAGS += -fcheck-pointer-bounds -mmpx
+ endif
+- CFLAGS += $(BASEFLAGS)
+- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
$(CFLAGS)
+- LDFLAGS := -g
++ CXXFLAGS += $(BASEFLAGS)
++ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector
++ LDFLAGS ?= -g
+ #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS)
+ LIBS := -lasan -lubsan -ldl $(LIBS)
+ else
+@@ -55,26 +56,26 @@
+ # GMEMTRACE=1
+ #endif
+ #--- just plain debug build ---
+- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
+- LDFLAGS = -g
++ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
++ LDFLAGS += -g
+ LIBS =
+ endif
+ endif
+
+ %.o : %.c
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cc
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.C
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cpp
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ %.o : %.cxx
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ # C/C++ linker
+
diff --git a/sci-biology/gffcompare/gffcompare-0.10.5.ebuild
b/sci-biology/gffcompare/gffcompare-0.10.5.ebuild
new file mode 100644
index 000000000..0b842d240
--- /dev/null
+++ b/sci-biology/gffcompare/gffcompare-0.10.5.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Compare, classify, merge, track, annotate GFF files"
+HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
+ https://github.com/gpertea/gffcompare";
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz ->
gclib-0.10.2.tar.gz"
+
+LICENSE="MIT Artistic-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# this cannot just depend on sci-biology/gclib (headers), the code inside
+# gclib needs to be compiled and objects get included inside gffcompare
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/Makefile.patch )
+
+src_compile(){
+ GCLIB=../gclib-0.10.2 emake
+}
+
+src_install(){
+ dobin gffcompare
+ dodoc README.md
+}
diff --git a/sci-biology/gffcompare/metadata.xml
b/sci-biology/gffcompare/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/gffcompare/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <maintainer type="person">
+ <email>[email protected]</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>[email protected]</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
