1 |
commit: ccf76cecc1842711fbbd1632aae79d5fd70f8045 |
2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Feb 25 22:37:57 2017 +0000 |
4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
5 |
CommitDate: Sat Feb 25 22:40:00 2017 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ccf76cec |
7 |
|
8 |
sci-biology/prodigal: Version bump to 2.6.3 |
9 |
|
10 |
Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
11 |
|
12 |
sci-biology/prodigal/Manifest | 1 + |
13 |
.../files/prodigal-2.6.3-fix-build-system.patch | 45 ++++++++++++++++++++++ |
14 |
sci-biology/prodigal/prodigal-2.6.3.ebuild | 27 +++++++++++++ |
15 |
3 files changed, 73 insertions(+) |
16 |
|
17 |
diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest |
18 |
index efc235beb4..f689f26e0f 100644 |
19 |
--- a/sci-biology/prodigal/Manifest |
20 |
+++ b/sci-biology/prodigal/Manifest |
21 |
@@ -1,2 +1,3 @@ |
22 |
+DIST prodigal-2.6.3.tar.gz 610934 SHA256 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 WHIRLPOOL d218510194777a15699cde33641768b24844e2077a1f63274a9d02c0d494c0d854dbbcf638df92839acd89916af63267d8e50b307a325f2e8026023675050fec |
23 |
DIST prodigal.v2_50.tar.gz 496654 SHA256 0220dcc740c49941f9c2536b3aa81d3193f885bfd05c694f805d90d2cefbc421 SHA512 b0f513148d9db7a5e29df010db535ea73b6609094f7a8753c5fccca821ee7b2b326a88b32ab3931e937df76f0cd4451f08d3449cf845f95d98557e44f9b8b923 WHIRLPOOL eb57b0448fd12c95ef54e09e374caed602c71c5deed90ded65ab8cf605494a0032b183cb293a5e6e4560f6e1beb4198333d2868ed53181a749778cafd5c49ab5 |
24 |
DIST prodigal.v2_60.tar.gz 615326 SHA256 f18b093e0ac3b9ba40fc4d7bb76c2e20f2edb6d265451c82e3396138c9aac331 SHA512 35441bbc36982c82389cb7f5060513b8be7686ef3f4328f63ea16c57d5914b7e7a25602b488769967fd759793784f6e44dce78c8eb1dd5ab739610031cd7fc81 WHIRLPOOL 2a866a81de298f0e7f225c345e9a4a0e851c179988825404f99964af6023ec22b1c5e117c847f30a0da510f4b78a5a9c3cab56105099ee5428a4eea276afa11a |
25 |
|
26 |
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 |
27 |
new file mode 100644 |
28 |
index 0000000000..b6d92392d1 |
29 |
--- /dev/null |
30 |
+++ b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch |
31 |
@@ -0,0 +1,45 @@ |
32 |
+Fix build system to honour user variables. |
33 |
+ |
34 |
+--- a/Makefile |
35 |
++++ b/Makefile |
36 |
+@@ -19,32 +19,31 @@ |
37 |
+ ############################################################################## |
38 |
+ |
39 |
+ SHELL = /bin/sh |
40 |
+-CC = gcc |
41 |
++CC ?= gcc |
42 |
+ |
43 |
+-CFLAGS += -pedantic -Wall -O3 |
44 |
+-LFLAGS = -lm $(LDFLAGS) |
45 |
++LIBS = -lm |
46 |
+ |
47 |
+ TARGET = prodigal |
48 |
+ SOURCES = $(shell echo *.c) |
49 |
+ HEADERS = $(shell echo *.h) |
50 |
+ OBJECTS = $(SOURCES:.c=.o) |
51 |
+ |
52 |
+-INSTALLDIR = /usr/local/bin |
53 |
++BINDIR = $(EPREFIX)/usr/bin |
54 |
+ |
55 |
+ all: $(TARGET) |
56 |
+ |
57 |
+ $(TARGET): $(OBJECTS) |
58 |
+- $(CC) $(CFLAGS) -o $@ $^ $(LFLAGS) |
59 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) |
60 |
+ |
61 |
+ %.o: %.c $(HEADERS) |
62 |
+- $(CC) $(CFLAGS) -c -o $@ $< |
63 |
++ $(CC) -Wall -pedantic $(CFLAGS) $(CPPFLAGS) -c -o $@ $< |
64 |
+ |
65 |
+ install: $(TARGET) |
66 |
+- install -d -m 0755 $(INSTALLDIR) |
67 |
+- install -m 0755 $(TARGET) $(INSTALLDIR) |
68 |
++ install -d -m 0755 $(DESTDIR)$(BINDIR) |
69 |
++ install -m 0755 $(TARGET) $(DESTDIR)$(BINDIR) |
70 |
+ |
71 |
+ uninstall: |
72 |
+- -rm $(INSTALLDIR)/$(TARGET) |
73 |
++ -rm $(DESTDIR)$(BINDIR)/$(TARGET) |
74 |
+ |
75 |
+ clean: |
76 |
+ -rm -f $(OBJECTS) |
77 |
|
78 |
diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3.ebuild |
79 |
new file mode 100644 |
80 |
index 0000000000..1eb3a64732 |
81 |
--- /dev/null |
82 |
+++ b/sci-biology/prodigal/prodigal-2.6.3.ebuild |
83 |
@@ -0,0 +1,27 @@ |
84 |
+# Copyright 1999-2017 Gentoo Foundation |
85 |
+# Distributed under the terms of the GNU General Public License v2 |
86 |
+# $Id$ |
87 |
+ |
88 |
+EAPI=6 |
89 |
+ |
90 |
+inherit toolchain-funcs |
91 |
+ |
92 |
+DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" |
93 |
+HOMEPAGE="http://prodigal.ornl.gov/" |
94 |
+SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" |
95 |
+ |
96 |
+LICENSE="GPL-3" |
97 |
+SLOT="0" |
98 |
+KEYWORDS="~amd64" |
99 |
+IUSE="" |
100 |
+ |
101 |
+DEPEND="" |
102 |
+RDEPEND="" |
103 |
+ |
104 |
+S=${WORKDIR}/${P^} |
105 |
+ |
106 |
+PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) |
107 |
+ |
108 |
+src_configure() { |
109 |
+ tc-export CC |
110 |
+} |