summaryrefslogtreecommitdiff
blob: d449af190b42de39488c6cd215326897d442372f (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
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

EAPI=7
PYTHON_COMPAT=( python3_{6..9} )

inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg

DESCRIPTION="Visual Molecular Dynamics"
HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"

MY_PV="${PV/_alpha/a}"
MY_P="${PN}-${MY_PV}"
SRC_URI="
	${MY_P}.src.tar
	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
	https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch
"

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"

CDEPEND="
	>=dev-lang/tk-8.6.1:0=
	dev-lang/perl
	dev-libs/expat
	$(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_USEDEP}]')
	sci-libs/netcdf:0=
	virtual/opengl
	>=x11-libs/fltk-1.1.10-r2:1
	x11-libs/libXft
	x11-libs/libXi
	${PYTHON_DEPS}
	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
	sqlite? ( dev-db/sqlite:3= )
	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
	xinerama? ( x11-libs/libXinerama )
"
DEPEND="${CDEPEND}"
BDEPEND="
	virtual/pkgconfig
	dev-lang/swig
"
RDEPEND="${CDEPEND}
	sci-biology/stride
	sci-chemistry/chemical-mime-data
	sci-chemistry/surf
	x11-terms/xterm
	msms? ( sci-chemistry/msms-bin )
	povray? ( media-gfx/povray )
"

S="${WORKDIR}/${MY_P}"

VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
# Binary only plugin!!
QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"

pkg_nofetch() {
	elog "Please download ${MY_P}.src.tar from"
	elog "${VMD_DOWNLOAD}"
	elog "after agreeing to the license and get"
	elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz"
	elog "Place both into your DISTDIR directory"
	elog
	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
	elog "file may get downloaded as a compressed tarball or not. In that case"
	elog "you will need to ensure you uncompress the file and rename it"
	elog "to ${MY_P}.src.tar"
}

src_prepare() {
	# Apply user patches from ${WORKDIR} to allow patching on patches
	# subdir too
	cd "${WORKDIR}"
	xdg_src_prepare

	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
	eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch

	use cuda && cuda_sanitize

	# Prepare plugins
	cd plugins || die

	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

	eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch

	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
	eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.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 $(fltk-config --libs)):g" \
		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):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"
	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' "${WORKDIR}"/vmd.desktop || die
	# Open PDB files with VMD
	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
	domenu "${WORKDIR}"/vmd.desktop
}