| 1 |
jlec 11/01/01 08:57:35 |
| 2 |
|
| 3 |
Modified: ChangeLog |
| 4 |
Added: ccp4-apps-6.1.3-r6.ebuild |
| 5 |
Log: |
| 6 |
Fit sci-libs/ccp4-libs-6.1.3-r5 |
| 7 |
|
| 8 |
(Portage version: 2.2.0_alpha10/cvs/Linux x86_64) |
| 9 |
|
| 10 |
Revision Changes Path |
| 11 |
1.19 sci-chemistry/ccp4-apps/ChangeLog |
| 12 |
|
| 13 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.19&view=markup |
| 14 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.19&content-type=text/plain |
| 15 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?r1=1.18&r2=1.19 |
| 16 |
|
| 17 |
Index: ChangeLog |
| 18 |
=================================================================== |
| 19 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v |
| 20 |
retrieving revision 1.18 |
| 21 |
retrieving revision 1.19 |
| 22 |
diff -u -r1.18 -r1.19 |
| 23 |
--- ChangeLog 31 Dec 2010 17:17:35 -0000 1.18 |
| 24 |
+++ ChangeLog 1 Jan 2011 08:57:34 -0000 1.19 |
| 25 |
@@ -1,6 +1,11 @@ |
| 26 |
# ChangeLog for sci-chemistry/ccp4-apps |
| 27 |
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 |
| 28 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.18 2010/12/31 17:17:35 jlec Exp $ |
| 29 |
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
| 30 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.19 2011/01/01 08:57:34 jlec Exp $ |
| 31 |
+ |
| 32 |
+*ccp4-apps-6.1.3-r6 (01 Jan 2011) |
| 33 |
+ |
| 34 |
+ 01 Jan 2011; Justin Lecher <jlec@g.o> +ccp4-apps-6.1.3-r6.ebuild: |
| 35 |
+ Fit sci-libs/ccp4-libs-6.1.3-r5 |
| 36 |
|
| 37 |
31 Dec 2010; Justin Lecher <jlec@g.o> ccp4-apps-6.1.3-r5.ebuild: |
| 38 |
Block new ccp4-libs version |
| 39 |
|
| 40 |
|
| 41 |
|
| 42 |
1.1 sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild |
| 43 |
|
| 44 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild?rev=1.1&view=markup |
| 45 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild?rev=1.1&content-type=text/plain |
| 46 |
|
| 47 |
Index: ccp4-apps-6.1.3-r6.ebuild |
| 48 |
=================================================================== |
| 49 |
# Copyright 1999-2011 Gentoo Foundation |
| 50 |
# Distributed under the terms of the GNU General Public License v2 |
| 51 |
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r6.ebuild,v 1.1 2011/01/01 08:57:34 jlec Exp $ |
| 52 |
|
| 53 |
EAPI="3" |
| 54 |
|
| 55 |
PYTHON_DEPEND="2" |
| 56 |
|
| 57 |
inherit autotools eutils flag-o-matic gnuconfig python toolchain-funcs |
| 58 |
|
| 59 |
MY_P="${PN/-apps}-${PV}" |
| 60 |
|
| 61 |
SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
| 62 |
|
| 63 |
#UPDATE="04_03_09" |
| 64 |
#PATCHDATE="090511" |
| 65 |
|
| 66 |
PATCH_TOT="0" |
| 67 |
# Here's a little scriptlet to generate this list from the provided |
| 68 |
# index.patches file |
| 69 |
# |
| 70 |
# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; |
| 71 |
# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < |
| 72 |
# index.patches |
| 73 |
#PATCH1=( src/topp_ |
| 74 |
#topp.f-r1.16.2.5-r1.16.2.6.diff ) |
| 75 |
#PATCH2=( . |
| 76 |
#configure-r1.372.2.18-r1.372.2.19.diff ) |
| 77 |
|
| 78 |
DESCRIPTION="Protein X-ray crystallography toolkit" |
| 79 |
HOMEPAGE="http://www.ccp4.ac.uk/" |
| 80 |
RESTRICT="mirror" |
| 81 |
SRC_URI=" |
| 82 |
${SRC}/${PV}/${MY_P}-core-src.tar.gz |
| 83 |
http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" |
| 84 |
# patch tarball from upstream |
| 85 |
[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
| 86 |
# patches created by us |
| 87 |
[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
| 88 |
|
| 89 |
for i in $(seq $PATCH_TOT); do |
| 90 |
NAME="PATCH${i}[1]" |
| 91 |
SRC_URI="${SRC_URI} |
| 92 |
${SRC}/${PV}/patches/${!NAME}" |
| 93 |
done |
| 94 |
|
| 95 |
LICENSE="ccp4" |
| 96 |
SLOT="0" |
| 97 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
| 98 |
IUSE="examples X" |
| 99 |
|
| 100 |
X11DEPS=" |
| 101 |
x11-libs/libX11 |
| 102 |
x11-libs/libXaw |
| 103 |
x11-libs/libXt |
| 104 |
x11-libs/libxdl_view" |
| 105 |
|
| 106 |
TKDEPS=" |
| 107 |
>=dev-lang/tk-8.3 |
| 108 |
>=dev-tcltk/blt-2.4 |
| 109 |
dev-tcltk/iwidgets |
| 110 |
dev-tcltk/itcl |
| 111 |
dev-tcltk/itk |
| 112 |
>=dev-tcltk/tdom-0.8 |
| 113 |
dev-tcltk/tkimg |
| 114 |
dev-tcltk/tktreectrl" |
| 115 |
|
| 116 |
SCILIBS=" |
| 117 |
~sci-libs/ccp4-libs-${PV} |
| 118 |
>=sci-libs/ccp4-libs-${PV}-r5 |
| 119 |
sci-libs/clipper |
| 120 |
=sci-libs/fftw-2* |
| 121 |
sci-libs/mmdb |
| 122 |
virtual/blas |
| 123 |
virtual/lapack" |
| 124 |
|
| 125 |
SCIAPPS=" |
| 126 |
sci-chemistry/pdb-extract |
| 127 |
sci-chemistry/pymol |
| 128 |
sci-chemistry/rasmol |
| 129 |
>=sci-chemistry/oasis-4.0-r1" |
| 130 |
|
| 131 |
RDEPEND=" |
| 132 |
${TKDEPS} |
| 133 |
${SCILIBS} |
| 134 |
app-shells/tcsh |
| 135 |
dev-python/pyxml |
| 136 |
dev-libs/libxml2 |
| 137 |
dev-libs/libjwc_c |
| 138 |
dev-libs/libjwc_f |
| 139 |
dev-libs/boehm-gc |
| 140 |
!app-office/sc |
| 141 |
!<sci-chemistry/ccp4-6.1.2 |
| 142 |
X? ( ${X11DEPS} )" |
| 143 |
DEPEND="${RDEPEND} |
| 144 |
X? ( |
| 145 |
x11-misc/imake |
| 146 |
x11-proto/inputproto |
| 147 |
x11-proto/xextproto |
| 148 |
)" |
| 149 |
PDEPEND="${SCIAPPS}" |
| 150 |
|
| 151 |
S="${WORKDIR}/${MY_P}" |
| 152 |
|
| 153 |
pkg_setup() { |
| 154 |
python_set_active_version 2 |
| 155 |
} |
| 156 |
|
| 157 |
src_prepare() { |
| 158 |
einfo "Applying upstream patches ..." |
| 159 |
for patch in $(seq $PATCH_TOT); do |
| 160 |
base="PATCH${patch}" |
| 161 |
dir=$(eval echo \${${base}[0]}) |
| 162 |
p=$(eval echo \${${base}[1]}) |
| 163 |
pushd "${dir}" >& /dev/null |
| 164 |
ccp_patch "${DISTDIR}/${p}" |
| 165 |
popd >& /dev/null |
| 166 |
done |
| 167 |
einfo "Done." |
| 168 |
echo |
| 169 |
|
| 170 |
[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
| 171 |
|
| 172 |
einfo "Applying Gentoo patches ..." |
| 173 |
|
| 174 |
# it tries to create libdir, bindir etc on live system in configure |
| 175 |
ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
| 176 |
|
| 177 |
# We already have sci-chemistry/rasmol |
| 178 |
# Also remember to create the bindir. |
| 179 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch |
| 180 |
|
| 181 |
# libraries come from sci-libs/ccp4-libs |
| 182 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch |
| 183 |
|
| 184 |
# coreutils installs a binary called truncate |
| 185 |
# ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch |
| 186 |
# mv ./doc/truncate.doc ./doc/ftruncate.doc || die |
| 187 |
# mv ./html/truncate.html ./html/ftruncate.html || die |
| 188 |
|
| 189 |
# conflicts with media-libs/raptor |
| 190 |
# ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch |
| 191 |
# mv ./doc/rapper.doc ./doc/rappermc.doc || die |
| 192 |
# mv ./html/rapper.html ./html/rappermc.html || die |
| 193 |
|
| 194 |
# We have seperate ebuilds for those |
| 195 |
for bin in molref xia scala imosflm balbes; do |
| 196 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch |
| 197 |
done |
| 198 |
|
| 199 |
# don't configure what is not build |
| 200 |
ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch |
| 201 |
|
| 202 |
# Set python paths correctly |
| 203 |
ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch |
| 204 |
|
| 205 |
# Set python paths correctly |
| 206 |
ccp_patch "${FILESDIR}"/${PV}-pisa.patch |
| 207 |
|
| 208 |
# Set python paths correctly |
| 209 |
ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch |
| 210 |
|
| 211 |
# Fix upstreams code |
| 212 |
ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch |
| 213 |
|
| 214 |
# Update things for oasis 4 usage |
| 215 |
epatch "${WORKDIR}"/${PV}-oasis4.0.patch |
| 216 |
sed 's: oasis : :g' -i src/Makefile.in || die |
| 217 |
|
| 218 |
einfo "Done." # done applying Gentoo patches |
| 219 |
echo |
| 220 |
|
| 221 |
# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version |
| 222 |
sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure |
| 223 |
|
| 224 |
# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. |
| 225 |
pushd src/rapper 2>/dev/null |
| 226 |
sed -i \ |
| 227 |
-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \ |
| 228 |
configure.ac |
| 229 |
sed -i \ |
| 230 |
-e '/^SUBDIRS/s:libxml2 gc7.0::g' \ |
| 231 |
Makefile.am |
| 232 |
sed -i \ |
| 233 |
-e '/^rapper_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \ |
| 234 |
LOOP/Makefile.am |
| 235 |
sed -i \ |
| 236 |
-e "/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \ |
| 237 |
LOOP/Makefile.am |
| 238 |
eautoreconf |
| 239 |
popd 2>/dev/null |
| 240 |
|
| 241 |
gnuconfig_update |
| 242 |
|
| 243 |
python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py |
| 244 |
} |
| 245 |
|
| 246 |
src_configure() { |
| 247 |
# Build system is broken if we set LDFLAGS |
| 248 |
unset LDFLAGS |
| 249 |
|
| 250 |
# These are broken with ./src/procheck/ps.f |
| 251 |
filter-flags "-floop-*" |
| 252 |
|
| 253 |
# GENTOO_OSNAME can be one of: |
| 254 |
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
| 255 |
# linux_compaq_compilers linux_intel_compilers generic Darwin |
| 256 |
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
| 257 |
if [[ "$(tc-getFC)" = "ifort" ]]; then |
| 258 |
if use ia64; then |
| 259 |
GENTOO_OSNAME="ia64_linux_intel" |
| 260 |
else |
| 261 |
# Should be valid for x86, maybe amd64 |
| 262 |
GENTOO_OSNAME="linux_intel_compilers" |
| 263 |
fi |
| 264 |
else |
| 265 |
# Should be valid for x86 and amd64, at least |
| 266 |
GENTOO_OSNAME="linux" |
| 267 |
fi |
| 268 |
|
| 269 |
# Sets up env |
| 270 |
ln -s \ |
| 271 |
ccp4.setup-bash \ |
| 272 |
"${S}"/include/ccp4.setup |
| 273 |
|
| 274 |
# We agree to the license by emerging this, set in LICENSE |
| 275 |
sed -i \ |
| 276 |
-e "s~^\(^agreed=\).*~\1yes~g" \ |
| 277 |
"${S}"/configure |
| 278 |
|
| 279 |
# Fix up variables -- need to reset CCP4_MASTER at install-time |
| 280 |
sed -i \ |
| 281 |
-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
| 282 |
-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
| 283 |
-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 284 |
-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 285 |
-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
| 286 |
-e "s~^\(export CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
| 287 |
"${S}"/include/ccp4.setup* |
| 288 |
|
| 289 |
# Set up variables for build |
| 290 |
source "${S}"/include/ccp4.setup-sh |
| 291 |
|
| 292 |
export CC=$(tc-getCC) |
| 293 |
export CXX=$(tc-getCXX) |
| 294 |
export COPTIM=${CFLAGS} |
| 295 |
export CXXOPTIM=${CXXFLAGS} |
| 296 |
# Default to -O2 if FFLAGS is unset |
| 297 |
export FC=$(tc-getFC) |
| 298 |
export FOPTIM=${FFLAGS:- -O2} |
| 299 |
export BINSORT_SCR="${T}" |
| 300 |
export CCP4_MASTER="${WORKDIR}" |
| 301 |
export CCP4I_TCLTK="${EPREFIX}/usr/bin" |
| 302 |
|
| 303 |
# Can't use econf, configure rejects unknown options like --prefix |
| 304 |
./configure \ |
| 305 |
$(use_enable X x) \ |
| 306 |
--with-shared-libs \ |
| 307 |
--with-fftw="${EPREFIX}"/usr \ |
| 308 |
--with-warnings \ |
| 309 |
--disable-pdb_extract \ |
| 310 |
--disable-cctbx \ |
| 311 |
--disable-phaser \ |
| 312 |
--disable-diffractionImg \ |
| 313 |
--disable-clipper \ |
| 314 |
--disable-mosflm \ |
| 315 |
--disable-mrbump \ |
| 316 |
--tmpdir="${TMPDIR}" \ |
| 317 |
${GENTOO_OSNAME} || die "econf failed" |
| 318 |
|
| 319 |
# We do this manually, since disabling the clipper libraries also |
| 320 |
# disables the clipper programs |
| 321 |
pushd src/clipper_progs 2>/dev/null |
| 322 |
econf \ |
| 323 |
--prefix="${S}" \ |
| 324 |
--bindir="${ED}"/usr/libexec/ccp4/bin \ |
| 325 |
--with-ccp4="${S}" \ |
| 326 |
--with-clipper="${EPREFIX}"/usr \ |
| 327 |
--with-fftw="${EPREFIX}"/usr \ |
| 328 |
--with-mmdb="${EPREFIX}"/usr \ |
| 329 |
CXX=$(tc-getCXX) \ |
| 330 |
|| die |
| 331 |
popd 2>/dev/null |
| 332 |
} |
| 333 |
|
| 334 |
src_compile() { |
| 335 |
# fsplit is required for the programs |
| 336 |
pushd lib/src 2>/dev/null |
| 337 |
emake fsplit -j1 || die |
| 338 |
popd 2>/dev/null |
| 339 |
|
| 340 |
# We do this manually, since disabling the clipper libraries also |
| 341 |
# disables the clipper programs |
| 342 |
pushd src/clipper_progs 2>/dev/null |
| 343 |
emake || die |
| 344 |
popd 2>/dev/null |
| 345 |
|
| 346 |
emake -j1 || die "emake failed" |
| 347 |
} |
| 348 |
|
| 349 |
src_install() { |
| 350 |
# Set up variables for build |
| 351 |
source "${S}"/include/ccp4.setup-sh |
| 352 |
|
| 353 |
# make install || die "install failed" |
| 354 |
|
| 355 |
# if we don't make this, a ton of programs fail to install |
| 356 |
mkdir "${S}"/bin || die |
| 357 |
|
| 358 |
# We do this manually, since disabling the clipper libraries also |
| 359 |
# disables the clipper programs |
| 360 |
pushd "${S}"/src/clipper_progs 2>/dev/null |
| 361 |
emake install || die |
| 362 |
popd 2>/dev/null |
| 363 |
|
| 364 |
einstall || die "install failed" |
| 365 |
|
| 366 |
# Fix env |
| 367 |
# -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ |
| 368 |
# -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ |
| 369 |
sed -i \ |
| 370 |
-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \ |
| 371 |
-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ |
| 372 |
-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ |
| 373 |
-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \ |
| 374 |
-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ |
| 375 |
-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \ |
| 376 |
-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ |
| 377 |
-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ |
| 378 |
-e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ |
| 379 |
-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 380 |
-e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \ |
| 381 |
-e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \ |
| 382 |
-e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ |
| 383 |
-e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \ |
| 384 |
-e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ |
| 385 |
-e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \ |
| 386 |
-e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ |
| 387 |
-e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ |
| 388 |
-e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ |
| 389 |
-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 390 |
-e "/IMOSFLM_VERSION/d" \ |
| 391 |
"${S}"/include/ccp4.setup* || die |
| 392 |
|
| 393 |
# -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \ |
| 394 |
|
| 395 |
# Don't check for updates on every sourcing of /etc/profile |
| 396 |
sed -i \ |
| 397 |
-e "s:\(eval python.*\):#\1:g" |
| 398 |
"${S}"/include/ccp4.setup* || die |
| 399 |
|
| 400 |
# Collision with sci-chemistry/mrbump |
| 401 |
rm -f "${S}"/bin/{mrbump,pydbviewer} || die |
| 402 |
|
| 403 |
# Bins |
| 404 |
exeinto /usr/libexec/ccp4/bin/ |
| 405 |
doexe "${S}"/bin/* || die |
| 406 |
|
| 407 |
# Libs |
| 408 |
for file in "${S}"/lib/*; do |
| 409 |
if [[ -d ${file} ]]; then |
| 410 |
continue |
| 411 |
elif [[ -x ${file} ]]; then |
| 412 |
dolib.so ${file} || die |
| 413 |
else |
| 414 |
insinto /usr/$(get_libdir) |
| 415 |
doins ${file} || die |
| 416 |
fi |
| 417 |
done |
| 418 |
|
| 419 |
sed \ |
| 420 |
-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ |
| 421 |
-i "${S}"/include/ccp4.setup-sh || die |
| 422 |
|
| 423 |
# Setup scripts |
| 424 |
insinto /etc/profile.d |
| 425 |
# newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die |
| 426 |
newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die |
| 427 |
# newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die |
| 428 |
newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die |
| 429 |
rm -f "${S}"/include/ccp4.setup* |
| 430 |
|
| 431 |
# smartie -- log parsing |
| 432 |
insinto /usr/share/ccp4 |
| 433 |
doins -r "${S}"/share/smartie || die |
| 434 |
|
| 435 |
# Install docs and examples |
| 436 |
doman "${S}"/man/cat1/* |
| 437 |
|
| 438 |
mv "${S}"/manual/README "${S}"/manual/README-manual |
| 439 |
dodoc manual/* README CHANGES doc/* examples/README || die |
| 440 |
|
| 441 |
rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* |
| 442 |
rm "${ED}"/usr/share/doc/${PF}/COPYING.* |
| 443 |
|
| 444 |
dohtml -r "${S}"/html/* |
| 445 |
|
| 446 |
if use examples; then |
| 447 |
for i in data rnase toxd; do |
| 448 |
docinto examples/${i} |
| 449 |
dodoc "${S}"/examples/${i}/* |
| 450 |
done |
| 451 |
|
| 452 |
docinto examples/tutorial |
| 453 |
dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css |
| 454 |
for i in data results; do |
| 455 |
docinto examples/tutorial/${i} |
| 456 |
dodoc "${S}"/examples/tutorial/${i}/* |
| 457 |
done |
| 458 |
|
| 459 |
for i in non-runnable runnable; do |
| 460 |
docinto examples/unix/${i} |
| 461 |
dodoc "${S}"/examples/unix/${i}/* |
| 462 |
done |
| 463 |
fi |
| 464 |
# Needed for ccp4i docs to work |
| 465 |
dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die |
| 466 |
dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die |
| 467 |
|
| 468 |
# Fix overlaps with other packages |
| 469 |
rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die |
| 470 |
mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die |
| 471 |
mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die |
| 472 |
mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die |
| 473 |
|
| 474 |
cat >> "${T}"/baubles <<- EOF |
| 475 |
#!${EPREFIX}/bin/bash |
| 476 |
exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py |
| 477 |
EOF |
| 478 |
|
| 479 |
exeinto /usr/libexec/ccp4/bin/ |
| 480 |
doexe "${T}"/baubles || die |
| 481 |
} |
| 482 |
|
| 483 |
pkg_postinst() { |
| 484 |
einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" |
| 485 |
einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this." |
| 486 |
} |
| 487 |
|
| 488 |
# Epatch wrapper for bulk patching |
| 489 |
ccp_patch() { |
| 490 |
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
| 491 |
} |
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