blob: 81ebf51d9c20d8ce221bfe8ce6dc479225bdeb5a (
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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
|
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
DESCRIPTION="Visual Molecular Dynamics"
HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
SRC_URI="
https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
${P}.src.tar"
SLOT="0"
LICENSE="vmd"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RESTRICT="fetch"
# currently, tk-8.5* with USE=truetype breaks some
# tk apps such as Sequence Viewer or Timeline.
CDEPEND="
>=dev-lang/tk-8.6.1
dev-lang/perl
dev-libs/expat
dev-python/numpy[${PYTHON_USEDEP}]
sci-libs/netcdf:0=
virtual/opengl
>=x11-libs/fltk-1.1.10-r2:1
x11-libs/libXft
x11-libs/libXi
${PYTHON_DEPS}
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
sqlite? ( dev-db/sqlite:3= )
tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
xinerama? ( x11-libs/libXinerama )"
DEPEND="${CDEPEND}
virtual/pkgconfig
dev-lang/swig"
RDEPEND="${CDEPEND}
sci-biology/stride
sci-chemistry/surf
x11-terms/xterm
msms? ( sci-chemistry/msms-bin )
povray? ( media-gfx/povray )
"
VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
# Binary only plugin!!
QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
pkg_nofetch() {
elog "Please download ${P}.src.tar.gz from"
elog "${VMD_DOWNLOAD}"
elog "after agreeing to the license and get"
elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
elog "Place both in ${DISTDIR}"
}
src_prepare() {
use cuda && cuda_sanitize
epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
cd "${WORKDIR}"/plugins || die
epatch \
"${WORKDIR}"/${P}-gentoo-plugins.patch
[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
sed \
-e "s:CC = gcc:CC = $(tc-getCC):" \
-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
-e "s:-ltcl8.5:-ltcl:" \
-i Make-arch || die "Failed to set up plugins Makefile"
sed \
-e '/^AR /s:=:?=:g' \
-e '/^RANLIB /s:=:?=:g' \
-i ../plugins/*/Makefile || die
tc-export AR RANLIB
sed \
-e "s:\$(CXXFLAGS)::g" \
-i hesstrans/Makefile || die
# prepare vmd itself
cd "${S}" || die
epatch "${WORKDIR}"/${P}-gentoo-base.patch
# PREFIX
sed \
-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-i configure || die
sed \
-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-e "s:gentoo-gcc:$(tc-getCC):g" \
-e "s:gentoo-g++:$(tc-getCXX):g" \
-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-e "s:gentoo-cflags:${CFLAGS}:g" \
-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-e "s:gentoo-nvflags::g" \
-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-i configure || die
if use cuda; then
sed \
-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-i configure src/Makefile || die
sed \
-e '/compute_/d' \
-i configure || die
sed \
-e 's:-gencode .*code=sm_..::' \
-i src/Makefile || die
fi
sed \
-e "s:LINUXPPC:LINUX:g" \
-e "s:LINUXALPHA:LINUX:g" \
-e "s:LINUXAMD64:LINUX:g" \
-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
EMAKEOPTS=(
TCLINC="-I${EPREFIX}/usr/include"
TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
TCLLDFLAGS="-shared"
NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include"
NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
NETCDFDYNAMIC=1
EXPATINC="-I${EPREFIX}/usr/include"
EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
EXPATLDFLAGS="-shared"
EXPATDYNAMIC=1
)
if use gromacs; then
EMAKEOPTS+=(
TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
TNGINC="-I${EPREFIX}/usr/include"
TNGLDFLAGS="-shared"
TNGDYNAMIC=1
)
fi
if use sqlite; then
EMAKEOPTS+=(
SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
SQLITEINC="-I${EPREFIX}/usr/include"
SQLITELDFLAGS="-shared"
SQLITEDYNAMIC=1
)
fi
}
src_configure() {
local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
rm -f configure.options && echo $myconf >> configure.options
use cuda && myconf+=" CUDA"
# use mpi && myconf+=" MPI"
use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
use xinerama && myconf+=" XINERAMA"
export \
PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
PYTHON_LIBRARY="$(python_get_LIBS)" \
NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
perl ./configure LINUX \
${myconf} || die
}
src_compile() {
# build plugins
cd "${WORKDIR}"/plugins || die
emake \
${EMAKEOPTS[@]} \
LINUX
# build vmd
cd "${S}"/src || die
emake
}
src_install() {
# install plugins
cd "${WORKDIR}"/plugins || die
emake \
PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
distrib
# install vmd
cd "${S}"/src || die
emake install
# install docs
cd "${S}" || die
dodoc Announcement README doc/ig.pdf doc/ug.pdf
# remove some of the things we don't want and need in
# /usr/lib
cd "${ED}"/usr/$(get_libdir)/vmd || die
rm -fr doc README Announcement LICENSE || \
die "failed to clean up /usr/lib/vmd directory"
# adjust path in vmd wrapper
sed \
-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
|| die "failed to set up vmd wrapper script"
# install icon and generate desktop entry
insinto /usr/share/pixmaps
doins "${WORKDIR}"/vmd.png
eprefixify "${WORKDIR}"/vmd.desktop
sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
domenu "${WORKDIR}"/vmd.desktop
}
|
GitWeb