[gentoo-commits] repo/gentoo:master commit in: sci-biology/prodigal/, sci-biology/prodigal/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/prodigal/, sci-biology/prodigal/files/

[David Seifert]

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
+}