commit: ea003571ac74c209954bfe016cb6a91319058080
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 22:23:40 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 22:23:40 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea003571
sci-biology/gffread: new package
Does not compile, will report upstream.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/gffread/files/Makefile.patch | 39 +++++++++++++++++++++++++++++++
sci-biology/gffread/gffread-0.9.12.ebuild | 18 ++++++++++++++
sci-biology/gffread/metadata.xml | 12 ++++++++++
3 files changed, 69 insertions(+)
diff --git a/sci-biology/gffread/files/Makefile.patch
b/sci-biology/gffread/files/Makefile.patch
new file mode 100644
index 000000000..45f8c3ebd
--- /dev/null
+++ b/sci-biology/gffread/files/Makefile.patch
@@ -0,0 +1,39 @@
+--- gffread-0.9.12/Makefile 2018-06-26 00:05:05.298388489 +0200
++++ gffread-0.9.12/Makefile 2018-06-26 00:07:07.461729681 +0200
+@@ -1,4 +1,4 @@
+-GCLDIR := ../gclib
++GCLDIR := $(EPREFIX)/usr/include/gclib
+ SEARCHDIRS := -I. -I${GCLDIR}
+
+ SYSTYPE := $(shell uname)
+@@ -10,7 +10,7 @@
+ MARCH =
+ endif
+
+-CC := g++
++CXX ?= g++
+
+ BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
+ -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions
-fno-rtti
+@@ -26,15 +26,17 @@
+ GCC45OPTMAIN :=
+
+ ifeq ($(findstring release,$(MAKECMDGOALS)),release)
+- CFLAGS := -O2 -DNDEBUG $(BASEFLAGS)
++ CXXFLAGS ?= -O2
++ CXXFLAGS += -DNDEBUG $(BASEFLAGS)
+ LDFLAGS :=
+ else
+- CFLAGS := -g -DDEBUG $(BASEFLAGS)
+- LDFLAGS := -g
++ CXXFLAGS ?= -g
++ CXXFLAGS += -DDEBUG $(BASEFLAGS)
++ LDFLAGS ?= -g
+ endif
+
+ %.o : %.cpp
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CXX} ${CXXFLAGS} -c $< -o $@
+
+ # C/C++ linker
+
diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild
b/sci-biology/gffread/gffread-0.9.12.ebuild
new file mode 100644
index 000000000..968ebc256
--- /dev/null
+++ b/sci-biology/gffread/gffread-0.9.12.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract
regions from FASTA"
+HOMEPAGE="https://github.com/gpertea/gffread";
+SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/gclib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/Makefile.patch )
diff --git a/sci-biology/gffread/metadata.xml b/sci-biology/gffread/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/gffread/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>
