blob: 2922f57bfe3709ca154bf295c26aacae014febcb (
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
156
157
158
159
|
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=4
PYTHON_DEPEND="2"
AUTOTOOLS_AUTORECONF="true"
inherit autotools-utils python toolchain-funcs versionator
MY_S2_PV=$(replace_version_separator 2 - ${PV})
MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
MY_S_P=${MY_S2_P}-${PR/r/revision-}
MY_PV=${PV}
MY_P=${PN}-${MY_PV}
DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
SRC_URI="
http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )"
SLOT="0"
LICENSE="GPL-3"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
IUSE="+openmp static-libs test"
AUTOTOOLS_IN_SOURCE_BUILD=1
SCIDEPS="
>=sci-libs/ccp4-libs-6.1
sci-libs/clipper
>=sci-libs/coot-data-2
>=sci-libs/gsl-1.3
>=sci-libs/mmdb-1.23:0
sci-libs/ssm
<sci-libs/monomer-db-1
sci-chemistry/reduce
<sci-chemistry/refmac-5.6
sci-chemistry/probe"
XDEPS="
gnome-base/libgnomecanvas
gnome-base/librsvg:2
media-libs/libpng
media-libs/freeglut
x11-libs/gtk+:2
x11-libs/goocanvas:0
x11-libs/gtkglext"
SCHEMEDEPS="
dev-scheme/net-http
dev-scheme/guile-gui
>=dev-scheme/guile-lib-0.1.6
dev-scheme/guile-www
>=x11-libs/guile-gtk-2.1"
RDEPEND="
${SCIDEPS}
${XDEPS}
${SCHEMEDEPS}
dev-python/pygtk:2
>=dev-libs/gmp-4.2.2-r2
>=net-misc/curl-7.19.6
net-dns/libidn"
DEPEND="${RDEPEND}
>=sys-devel/libtool-2.4-r2
dev-lang/swig
sys-devel/bc
test? ( dev-scheme/greg )"
S="${WORKDIR}/${MY_P}"
pkg_setup() {
if use openmp; then
tc-has-openmp || die "Please use an OPENMP capable compiler"
fi
python_set_active_version 2
python_pkg_setup
}
PATCHES=(
"${FILESDIR}"/${P}-clipper-config.patch
"${FILESDIR}"/${P}-goocanvas.patch
"${FILESDIR}"/${P}-mmdb-config.patch
"${FILESDIR}"/${P}-ssm.patch
)
src_prepare() {
sed \
-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-i configure.in || die
autotools-utils_src_prepare
}
src_configure() {
# All the --with's are used to activate various parts.
# Yes, this is broken behavior.
local myeconfargs=(
--includedir='${prefix}/include/coot'
--with-goocanvas-prefix="${EPREFIX}/usr"
--with-guile
--with-python="${EPREFIX}/usr"
--with-guile-gtk
--with-gtk2
--with-pygtk
$(use_enable openmp)
)
autotools-utils_src_configure
}
src_test() {
source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
mkdir "${T}"/coot_test
export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
export COOT_SCHEME_DIR="${S}/scheme/"
export COOT_RESOURCES_FILE="${S}/cootrc"
export COOT_PIXMAPS_DIR="${S}/pixmaps/"
export COOT_DATA_DIR="${S}/"
export COOT_PYTHON_DIR="${S}/python/"
export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
export PYTHONHOME="${EPREFIX}"/usr/
export CCP4_SCR="${T}"/coot_test/
export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
export SYMINFO="${S}/syminfo.lib"
export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
cat > command-line-greg.scm <<- EOF
(use-modules (ice-9 greg))
(set! greg-tools (list "greg-tests"))
(set! greg-debug #t)
(set! greg-verbose 5)
(let ((r (greg-test-run)))
(if r
(coot-real-exit 0)
(coot-real-exit 1)))
EOF
einfo "Running test with following paths ..."
einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
einfo "COOT_DATA_DIR $COOT_DATA_DIR"
einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
einfo "PYTHONPATH $PYTHONPATH"
einfo "PYTHONHOME $PYTHONHOME"
einfo "CCP4_SCR ${CCP4_SCR}"
einfo "CLIBD_MON ${CLIBD_MON}"
einfo "SYMINFO ${SYMINFO}"
"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
}
|
GitWeb