blob: 976bbb856a162678b14a70d1331258da772f457b (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
|
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild,v 1.8 2011/06/21 16:02:05 jlec Exp $
EAPI="3"
PYTHON_DEPEND="2:2.5"
SUPPORT_PYTHON_ABIS="1"
PYTHON_EXPORT_PHASE_FUNCTIONS="1"
RESTRICT_PYTHON_ABIS="2.4 3.*"
inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator
MY_PV=$(get_version_component_range 1-2)
MY_P="${PN}-${MY_PV}"
DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
LICENSE="BSD"
HOMEPAGE="http://pdb2pqr.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
SLOT="0"
IUSE="doc examples opal"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
virtual/fortran
dev-python/numpy
sci-chemistry/openbabel
opal? ( dev-python/zsi )"
DEPEND="${RDEPEND}"
S="${WORKDIR}/${MY_P}"
src_prepare() {
epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
epatch "${FILESDIR}"/${PV}-install.patch
sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
|| die "Failed to fix Makefile.am"
python_src_prepare
preparation() {
eautoreconf
}
python_execute_function -s preparation
}
src_configure() {
# we need to compile the *.so as pic
append-flags -fPIC
FFLAGS="${FFLAGS} -fPIC"
configuration() {
# Avoid automagic to numeric
NUMPY="${EPREFIX}/$(python_get_sitedir)" \
F77="$(tc-getFC)" \
econf \
$(use_with opal)
}
python_execute_function -s configuration
}
src_compile() {
compilation() {
emake || die
}
python_execute_function -s compilation
}
src_test() {
testing() {
emake -j1 test \
|| die "tests failed"
}
python_execute_function -s testing
}
src_install() {
installation() {
dodir $(python_get_sitedir)/${PN}
emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
PREFIX="" install || die "install failed"
INPATH="$(python_get_sitedir)/${PN}"
# generate pdb2pqr wrapper
cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
#!/bin/sh
$(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$*
EOF
dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
insinto "${INPATH}"
doins __init__.py || \
die "Setting up the pdb2pqr site-package failed."
exeinto "${INPATH}"
doexe ${PN}.py || die "Installing pdb2pqr failed."
insinto "${INPATH}"/dat
doins dat/* || die "Installing data failed."
exeinto "${INPATH}"/extensions
doexe extensions/* || \
die "Failed to install extensions."
insinto "${INPATH}"/src
doins src/*.py || die "Installing of python scripts failed."
exeinto "${INPATH}"/propka
doexe propka/_propkalib.so || \
die "Failed to install propka."
insinto "${INPATH}"/propka
doins propka/propkalib.py propka/__init__.py || \
die "Failed to install propka."
insinto "${INPATH}"/pdb2pka
doins pdb2pka/*.{py,so,DAT,h} || \
die "Failed to install pdb2pka."
insinto "${INPATH}"/pdb2pka/
doins pdb2pka/*.{py,so,DAT,h} || \
die "Failed to install pdb2pka."
}
python_execute_function -s installation
dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
if use doc; then
cd doc
sh genpydoc.sh \
|| die "genpydoc failed"
dohtml -r *.html images pydoc \
|| die "failed to install html docs"
cd -
fi
if use examples; then
insinto /usr/share/${PN}/
doins -r examples || die "Failed to install examples."
fi
dodoc ChangeLog NEWS README AUTHORS || \
die "Failed to install docs"
}
pkg_postinst() {
python_mod_optimize ${PN}
}
pkg_postrm() {
python_mod_cleanup ${PN}
}
|
GitWeb