commit: ccf76cecc1842711fbbd1632aae79d5fd70f8045 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Feb 25 22:37:57 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Feb 25 22:40:00 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ccf76cec
sci-biology/prodigal: Version bump to 2.6.3 Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/prodigal/Manifest | 1 + .../files/prodigal-2.6.3-fix-build-system.patch | 45 ++++++++++++++++++++++ sci-biology/prodigal/prodigal-2.6.3.ebuild | 27 +++++++++++++ 3 files changed, 73 insertions(+) diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest index efc235beb4..f689f26e0f 100644 --- a/sci-biology/prodigal/Manifest +++ b/sci-biology/prodigal/Manifest @@ -1,2 +1,3 @@ +DIST prodigal-2.6.3.tar.gz 610934 SHA256 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 WHIRLPOOL d218510194777a15699cde33641768b24844e2077a1f63274a9d02c0d494c0d854dbbcf638df92839acd89916af63267d8e50b307a325f2e8026023675050fec DIST prodigal.v2_50.tar.gz 496654 SHA256 0220dcc740c49941f9c2536b3aa81d3193f885bfd05c694f805d90d2cefbc421 SHA512 b0f513148d9db7a5e29df010db535ea73b6609094f7a8753c5fccca821ee7b2b326a88b32ab3931e937df76f0cd4451f08d3449cf845f95d98557e44f9b8b923 WHIRLPOOL eb57b0448fd12c95ef54e09e374caed602c71c5deed90ded65ab8cf605494a0032b183cb293a5e6e4560f6e1beb4198333d2868ed53181a749778cafd5c49ab5 DIST prodigal.v2_60.tar.gz 615326 SHA256 f18b093e0ac3b9ba40fc4d7bb76c2e20f2edb6d265451c82e3396138c9aac331 SHA512 35441bbc36982c82389cb7f5060513b8be7686ef3f4328f63ea16c57d5914b7e7a25602b488769967fd759793784f6e44dce78c8eb1dd5ab739610031cd7fc81 WHIRLPOOL 2a866a81de298f0e7f225c345e9a4a0e851c179988825404f99964af6023ec22b1c5e117c847f30a0da510f4b78a5a9c3cab56105099ee5428a4eea276afa11a diff --git a/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch new file mode 100644 index 0000000000..b6d92392d1 --- /dev/null +++ b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch @@ -0,0 +1,45 @@ +Fix build system to honour user variables. + +--- a/Makefile ++++ b/Makefile +@@ -19,32 +19,31 @@ + ############################################################################## + + SHELL = /bin/sh +-CC = gcc ++CC ?= gcc + +-CFLAGS += -pedantic -Wall -O3 +-LFLAGS = -lm $(LDFLAGS) ++LIBS = -lm + + TARGET = prodigal + SOURCES = $(shell echo *.c) + HEADERS = $(shell echo *.h) + OBJECTS = $(SOURCES:.c=.o) + +-INSTALLDIR = /usr/local/bin ++BINDIR = $(EPREFIX)/usr/bin + + all: $(TARGET) + + $(TARGET): $(OBJECTS) +- $(CC) $(CFLAGS) -o $@ $^ $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + %.o: %.c $(HEADERS) +- $(CC) $(CFLAGS) -c -o $@ $< ++ $(CC) -Wall -pedantic $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + + install: $(TARGET) +- install -d -m 0755 $(INSTALLDIR) +- install -m 0755 $(TARGET) $(INSTALLDIR) ++ install -d -m 0755 $(DESTDIR)$(BINDIR) ++ install -m 0755 $(TARGET) $(DESTDIR)$(BINDIR) + + uninstall: +- -rm $(INSTALLDIR)/$(TARGET) ++ -rm $(DESTDIR)$(BINDIR)/$(TARGET) + + clean: + -rm -f $(OBJECTS) diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3.ebuild new file mode 100644 index 0000000000..1eb3a64732 --- /dev/null +++ b/sci-biology/prodigal/prodigal-2.6.3.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" +HOMEPAGE="http://prodigal.ornl.gov/"; +SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="" + +S=${WORKDIR}/${P^} + +PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) + +src_configure() { + tc-export CC +}
