1 |
commit: ccc801a7333bcbd8651af3bd00d42545e84aa07c |
2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Feb 25 18:44:32 2017 +0000 |
4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
5 |
CommitDate: Sat Feb 25 19:18:20 2017 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ccc801a7 |
7 |
|
8 |
sci-biology/amos: Use python-single-r1 instead of python-r1 |
9 |
|
10 |
* Make build system parallel buildable |
11 |
* Make build system honour AR properly |
12 |
|
13 |
Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
14 |
|
15 |
sci-biology/amos/amos-3.1.0-r3.ebuild | 49 +++++++++ |
16 |
.../amos/files/amos-3.1.0-fix-build-system.patch | 116 +++++++++++++++++++++ |
17 |
2 files changed, 165 insertions(+) |
18 |
|
19 |
diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild |
20 |
new file mode 100644 |
21 |
index 0000000000..aa59d60a3b |
22 |
--- /dev/null |
23 |
+++ b/sci-biology/amos/amos-3.1.0-r3.ebuild |
24 |
@@ -0,0 +1,49 @@ |
25 |
+# Copyright 1999-2017 Gentoo Foundation |
26 |
+# Distributed under the terms of the GNU General Public License v2 |
27 |
+# $Id$ |
28 |
+ |
29 |
+EAPI=6 |
30 |
+ |
31 |
+PYTHON_COMPAT=( python2_7 ) |
32 |
+ |
33 |
+inherit autotools flag-o-matic python-single-r1 |
34 |
+ |
35 |
+DESCRIPTION="A Modular, Open-Source whole genome assembler" |
36 |
+HOMEPAGE="http://amos.sourceforge.net/" |
37 |
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz |
38 |
+ https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" |
39 |
+ |
40 |
+LICENSE="Artistic" |
41 |
+SLOT="0" |
42 |
+KEYWORDS="~amd64 ~x86" |
43 |
+IUSE="qt4" |
44 |
+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
45 |
+ |
46 |
+DEPEND="qt4? ( dev-qt/qtcore:4 )" |
47 |
+RDEPEND="${DEPEND} |
48 |
+ ${PYTHON_DEPS} |
49 |
+ dev-perl/DBI |
50 |
+ dev-perl/Statistics-Descriptive |
51 |
+ sci-biology/mummer" |
52 |
+ |
53 |
+PATCHES=( |
54 |
+ "${FILESDIR}"/${P}-gcc-4.7.patch |
55 |
+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch |
56 |
+ "${WORKDIR}"/${P}-fix-c++14.patch |
57 |
+ "${FILESDIR}"/${P}-qa-Wformat.patch |
58 |
+ "${FILESDIR}"/${P}-fix-build-system.patch |
59 |
+) |
60 |
+ |
61 |
+src_prepare() { |
62 |
+ default |
63 |
+ eautoreconf |
64 |
+ |
65 |
+ # prevent GCC 6 log pollution due |
66 |
+ # to hash_map deprecation in C++11 |
67 |
+ append-cxxflags -Wno-cpp |
68 |
+} |
69 |
+ |
70 |
+src_install() { |
71 |
+ default |
72 |
+ python_fix_shebang "${ED%/}"/usr/bin/goBambus2 |
73 |
+} |
74 |
|
75 |
diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch |
76 |
new file mode 100644 |
77 |
index 0000000000..9c824dd2f1 |
78 |
--- /dev/null |
79 |
+++ b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch |
80 |
@@ -0,0 +1,116 @@ |
81 |
+* Use proper AR and not just 'ar' |
82 |
+* Fix build system to build in parallel |
83 |
+ |
84 |
+--- a/configure.ac |
85 |
++++ b/configure.ac |
86 |
+@@ -34,6 +34,7 @@ |
87 |
+ AC_PROG_INSTALL |
88 |
+ AC_PROG_LN_S |
89 |
+ AC_PROG_RANLIB |
90 |
++AM_PROG_AR |
91 |
+ AC_PROG_CPP |
92 |
+ AC_PATH_PROG(PERL, [perl], [:]) |
93 |
+ AC_PATH_PROG(PYTHON, [python], [:]) |
94 |
+--- a/src/Align/Makefile.am |
95 |
++++ b/src/Align/Makefile.am |
96 |
+@@ -133,7 +133,7 @@ |
97 |
+ |
98 |
+ ##-- hash-overlap |
99 |
+ hash_overlap_LDADD = \ |
100 |
+- $(top_builddir)/src/Align/libAlign.a \ |
101 |
++ libAlign.a \ |
102 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
103 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
104 |
+ $(top_builddir)/src/Common/libCommon.a \ |
105 |
+@@ -172,7 +172,7 @@ |
106 |
+ |
107 |
+ ##-- make-consensus |
108 |
+ make_consensus_LDADD = \ |
109 |
+- $(top_builddir)/src/Align/libAlign.a \ |
110 |
++ libAlign.a \ |
111 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
112 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
113 |
+ $(top_builddir)/src/Common/libCommon.a \ |
114 |
+@@ -182,7 +182,7 @@ |
115 |
+ |
116 |
+ ##-- make-consensus_poly |
117 |
+ make_consensus_poly_LDADD = \ |
118 |
+- $(top_builddir)/src/Align/libAlign_poly.a \ |
119 |
++ libAlign_poly.a \ |
120 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
121 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
122 |
+ $(top_builddir)/src/Common/libCommon.a \ |
123 |
+@@ -192,7 +192,7 @@ |
124 |
+ |
125 |
+ ##-- maligntest |
126 |
+ maligntest_LDADD = \ |
127 |
+- $(top_builddir)/src/Align/libAlign.a \ |
128 |
++ libAlign.a \ |
129 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
130 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
131 |
+ $(top_builddir)/src/Common/libCommon.a \ |
132 |
+@@ -202,7 +202,7 @@ |
133 |
+ |
134 |
+ ##-- merge-contigs |
135 |
+ merge_contigs_LDADD = \ |
136 |
+- $(top_builddir)/src/Align/libAlign.a \ |
137 |
++ libAlign.a \ |
138 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
139 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
140 |
+ $(top_builddir)/src/Common/libCommon.a \ |
141 |
+@@ -235,7 +235,7 @@ |
142 |
+ |
143 |
+ ##-- show-ma-asm |
144 |
+ show_ma_asm_LDADD = \ |
145 |
+- $(top_builddir)/src/Align/libAlign.a \ |
146 |
++ libAlign.a \ |
147 |
+ $(top_builddir)/src/Common/libCommon.a \ |
148 |
+ $(top_builddir)/src/AMOS/libAMOS.a |
149 |
+ show_ma_asm_SOURCES = \ |
150 |
+@@ -261,7 +261,7 @@ |
151 |
+ |
152 |
+ ##-- simple-overlap |
153 |
+ simple_overlap_LDADD = \ |
154 |
+- $(top_builddir)/src/Align/libAlign.a \ |
155 |
++ libAlign.a \ |
156 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
157 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
158 |
+ $(top_builddir)/src/Common/libCommon.a \ |
159 |
+@@ -272,7 +272,7 @@ |
160 |
+ |
161 |
+ ##-- test-align |
162 |
+ test_align_LDADD = \ |
163 |
+- $(top_builddir)/src/Align/libAlign.a \ |
164 |
++ libAlign.a \ |
165 |
+ $(top_builddir)/src/CelMsg/libCelMsg.a \ |
166 |
+ $(top_builddir)/src/Slice/libSlice.a \ |
167 |
+ $(top_builddir)/src/Common/libCommon.a \ |
168 |
+--- a/src/Bambus/Bundler/Makefile.am |
169 |
++++ b/src/Bambus/Bundler/Makefile.am |
170 |
+@@ -47,7 +47,7 @@ |
171 |
+ clk.cc |
172 |
+ |
173 |
+ MarkRepeats_LDADD = \ |
174 |
+- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ |
175 |
++ libBundler.a \ |
176 |
+ $(top_builddir)/src/Common/libCommon.a \ |
177 |
+ $(top_builddir)/src/AMOS/libAMOS.a \ |
178 |
+ $(top_builddir)/src/GNU/libGNU.a |
179 |
+@@ -55,7 +55,7 @@ |
180 |
+ MarkRepeats.cc |
181 |
+ |
182 |
+ OrientContigs_LDADD = \ |
183 |
+- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ |
184 |
++ libBundler.a \ |
185 |
+ $(top_builddir)/src/Common/libCommon.a \ |
186 |
+ $(top_builddir)/src/AMOS/libAMOS.a \ |
187 |
+ $(top_builddir)/src/GNU/libGNU.a |
188 |
+@@ -63,7 +63,7 @@ |
189 |
+ OrientContigs.cc |
190 |
+ |
191 |
+ FilterEdgesByCluster_LDADD = \ |
192 |
+- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ |
193 |
++ libBundler.a \ |
194 |
+ $(top_builddir)/src/Common/libCommon.a \ |
195 |
+ $(top_builddir)/src/AMOS/libAMOS.a \ |
196 |
+ $(top_builddir)/src/GNU/libGNU.a |