diff options
| author |   Justin Lecher (jlec) <jlec@j-schmitz.net> | 2010-02-06 01:25:07 +0100 |
|---|---|---|
| committer | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2010-02-07 00:55:37 +0100 |
| commit | bb069236178e3649ad9b33f9cd538ddfa0337863 (patch) | |
| tree | ecaad1fdc4efa13767d16454a87d7d193123a7cb | |
| parent | InCvs (diff) | |
| download | sci-bb069236178e3649ad9b33f9cd538ddfa0337863.tar.gz sci-bb069236178e3649ad9b33f9cd538ddfa0337863.tar.bz2 sci-bb069236178e3649ad9b33f9cd538ddfa0337863.zip | |
InCvs
22 files changed, 0 insertions, 810 deletions
diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog deleted file mode 100644 index 80eede99c..000000000 --- a/sci-chemistry/ccp4i/ChangeLog +++ /dev/null @@ -1,132 +0,0 @@ -# ChangeLog for sci-chemistry/ccp4i -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*ccp4i-6.1.3-r1 (30 Jan 2010) - - 30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net> - -ccp4i-6.1.3.ebuild, +ccp4i-6.1.3-r1.ebuild: - Bad upstream, changed tarball w/o bumping - -*ccp4i-6.1.3 (22 Dec 2009) - - 22 Dec 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.3-fix-baubles.patch, +ccp4i-6.1.3.ebuild, - +files/6.1.3-rename-rapper.patch, +files/6.1.3-rename-superpose.patch, - +files/6.1.3-rename-truncate.patch: - Version bump - -*ccp4i-6.1.2-r7 (22 Nov 2009) - - 22 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +ccp4i-6.1.2-r7.ebuild: - Do not install bundled imosflm - - 17 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - ccp4i-6.1.2-r6.ebuild, metadata.xml: - oasis4 use removed again - -*ccp4i-6.1.2-r6 (15 Nov 2009) - - 15 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +ccp4i-6.1.2-r6.ebuild: - added oasis-4 support - -*ccp4i-6.1.2-r5 (02 Nov 2009) - - 02 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.2-fix-f2mtz.patch, +ccp4i-6.1.2-r5.ebuild: - f2mtz fix - upstream #4061 - b.g.o. 289379 - -*ccp4i-6.1.2-r4 (29 Sep 2009) - - 29 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - -ccp4i-6.1.2-r3.ebuild, +ccp4i-6.1.2-r4.ebuild: - It should have been bumped before - -*ccp4i-6.1.2-r3 (02 Sep 2009) - - 02 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.2-crank_shelxd.tcl.patch, -ccp4i-6.1.1-r1.ebuild, - -ccp4i-6.1.1-r3.ebuild, -ccp4i-6.1.1-r4.ebuild, -ccp4i-6.1.2-r2.ebuild, - +ccp4i-6.1.2-r3.ebuild: - added crank_shelxd.tcl.patch - QA rmoved WINDOWS and UNIX binary dirs - cleaned up old versions - -*ccp4i-6.1.2-r2 (17 Aug 2009) - - 17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +ccp4i-6.1.2-r2.ebuild, -ccp4i-6.1.2-r1.ebuild: - fix for collision with mrbump - -*ccp4i-6.1.2-r1 (14 Aug 2009) - - 14 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - -ccp4i-6.1.2.ebuild, +ccp4i-6.1.2-r1.ebuild: - some fixes to remove imosflm - -*ccp4i-6.1.2 (29 Jul 2009) - - 29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.2-fix-baubles.patch, +ccp4i-6.1.2.ebuild, - +files/6.1.2-rename-rapper.patch, +files/6.1.2-rename-superpose.patch, - +files/6.1.2-rename-truncate.patch: - this is still not released - - 07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - ccp4i-6.1.1-r5.ebuild: - added media-gfx/graphviz as dep - -*ccp4i-6.1.1-r5 (07 Jul 2009) - - 07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.1-fix-baubles.patch, +ccp4i-6.1.1-r5.ebuild: - fixes baubles path - -*ccp4i-6.1.1-r4 (05 Jul 2009) - - 05 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.1-rename-superpose.patch, +ccp4i-6.1.1-r4.ebuild: - superpose renamed to superpose-ccp4 - - 13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - -ccp4i-6.1.1.ebuild, -ccp4i-6.1.1-r2.ebuild: - cleaned up - -*ccp4i-6.1.1-r3 (13 May 2009) - - 13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +ccp4i-6.1.1-r3.ebuild: - Includes upstream updates src files from 03/04/09 - fixes bug 269504 - - 13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - ccp4i-6.1.1-r2.ebuild: - some QAs fixes - -*ccp4i-6.1.1-r2 (27 Mar 2009) - - 27 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.1-refmac.tcl.patch, +ccp4i-6.1.1-r2.ebuild: - latest refmac5.tcl update included - - 12 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/6.1.1-rename-rapper.patch, ccp4i-6.1.1-r1.ebuild: - rapper conflict with media-libs/raptor resolved - -*ccp4i-6.1.1-r1 (05 Mar 2009) - - 05 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +ccp4i-6.1.1-r1.ebuild: - first patch set included - -*ccp4i-6.1.1 (20 Feb 2009) - - 20 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - -ccp4i-6.0.99e.ebuild, +ccp4i-6.1.1.ebuild: - Add to sci overlay - Thanks Donnie for splitting this of from ccp4 meta - diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest deleted file mode 100644 index 6cb5d7ede..000000000 --- a/sci-chemistry/ccp4i/Manifest +++ /dev/null @@ -1,38 +0,0 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -AUX 6.1.1-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934 SHA1 cdc8752026f3cdd96ee0fd6a3f558e0729f88a6a SHA256 37c217f339a46a6b830ce8e791cbd32655e31ab8d58267fb625e841e867402b4 -AUX 6.1.1-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728 -AUX 6.1.1-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 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metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) - -iEYEARECAAYFAktkPVkACgkQgAnW8HDreRZnAwCguO9IL/WREXANm3jjGyEuss3M -kyIAn3emJrDjZWIOmdpN4D/hJ8em6gLp -=64TT ------END PGP SIGNATURE----- diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.1-r5.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.1-r5.ebuild deleted file mode 100644 index d794e6ebe..000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.1-r5.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit multilib base - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -UPDATE="04_03_09" -PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit, graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz - ${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz - http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="ccp4" -IUSE="" - -RESTRICT="mirror" - -RDEPEND=">=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4 - app-shells/tcsh - media-gfx/graphviz" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch - "${FILESDIR}"/${PV}-rename-truncate.patch - "${FILESDIR}"/${PV}-rename-rapper.patch - "${FILESDIR}"/${PV}-rename-superpose.patch - "${FILESDIR}"/${PV}-fix-baubles.patch - ) - -src_prepare() { - base_src_prepare - - sed -i \ - -e "s:share smartie:share ccp4 smartie:g" \ - "${S}"/ccp4i/imosflm/src/processingwizard.tcl -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i || die - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* || die - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i || die -} diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.2-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.2-r4.ebuild deleted file mode 100644 index 3d6e4f50a..000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.2-r4.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit multilib base - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" -[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="ccp4" -IUSE="" - -RESTRICT="mirror" - -RDEPEND=">=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4 - app-shells/tcsh - media-gfx/graphviz" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PV}-rename-truncate.patch - "${FILESDIR}"/${PV}-rename-rapper.patch - "${FILESDIR}"/${PV}-rename-superpose.patch - "${FILESDIR}"/${PV}-fix-baubles.patch - "${FILESDIR}"/${PV}-crank_shelxd.tcl.patch - ) - -src_prepare() { - base_src_prepare - - sed -i \ - -e "s:share smartie:share ccp4 smartie:g" \ - "${S}"/ccp4i/imosflm/src/processingwizard.tcl - - [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # rm imosflm stuff - rm -rf "${S}"/ccp4i/{bin/imosflm,imoslfm} - - rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS - - # This is installed by mrbump - rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} - - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i || die - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* || die - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i || die -} diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild deleted file mode 100644 index 6fce8ba71..000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit multilib base - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" -[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="ccp4" -IUSE="" - -RESTRICT="mirror" - -RDEPEND=">=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4 - app-shells/tcsh - media-gfx/graphviz" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PV}-crank_shelxd.tcl.patch - "${FILESDIR}"/${PV}-rename-truncate.patch - "${FILESDIR}"/${PV}-rename-rapper.patch - "${FILESDIR}"/${PV}-rename-superpose.patch - "${FILESDIR}"/${PV}-fix-baubles.patch - "${FILESDIR}"/${PV}-fix-f2mtz.patch - ) - -src_prepare() { - base_src_prepare - - sed -i \ - -e "s:share smartie:share ccp4 smartie:g" \ - "${S}"/ccp4i/imosflm/src/processingwizard.tcl - - [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # rm imosflm stuff - rm -rf "${S}"/ccp4i/{bin/imosflm,imoslfm} - - rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS - - # This is installed by mrbump - rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} - - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i || die - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* || die - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i || die -} diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.2-r7.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.2-r7.ebuild deleted file mode 100644 index b18e4aaf2..000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.2-r7.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit multilib base - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI=" - ${SRC}/${PV}/${MY_P}-core-src.tar.gz - http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" -[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="ccp4" -IUSE="" - -RESTRICT="mirror" - -RDEPEND=" - app-shells/tcsh - media-gfx/graphviz - >=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PV}-crank_shelxd.tcl.patch - "${FILESDIR}"/${PV}-rename-truncate.patch - "${FILESDIR}"/${PV}-rename-rapper.patch - "${FILESDIR}"/${PV}-rename-superpose.patch - "${FILESDIR}"/${PV}-fix-baubles.patch - "${FILESDIR}"/${PV}-fix-f2mtz.patch - ) - -src_prepare() { - base_src_prepare - - sed -i \ - -e "s:share smartie:share ccp4 smartie:g" \ - "${S}"/ccp4i/imosflm/src/processingwizard.tcl - - [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch - - epatch "${WORKDIR}"/${PV}-oasis4.0.patch -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # rm imosflm stuff - rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} - - rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS - - # This is installed by mrbump - rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} - - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i || die - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* || die - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i || die -} diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild deleted file mode 100644 index d30c3938f..000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r1.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit multilib base - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI=" - ${SRC}/${PV}/${MY_P}-core-src.tar.gz - http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" -[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="ccp4" -IUSE="" - -RESTRICT="mirror" - -RDEPEND=" - app-shells/tcsh - media-gfx/graphviz - >=dev-lang/tk-8.3 - >=dev-tcltk/blt-2.4" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PV}-rename-truncate.patch - "${FILESDIR}"/${PV}-rename-rapper.patch - "${FILESDIR}"/${PV}-rename-superpose.patch - "${FILESDIR}"/${PV}-fix-baubles.patch - ) - -src_prepare() { - base_src_prepare - - [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch - - epatch "${WORKDIR}"/${PV}-oasis4.0.patch -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # rm imosflm stuff - rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} - - rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS - - # This is installed by mrbump - rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} - - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i || die - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* || die - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i || die -} diff --git a/sci-chemistry/ccp4i/files/6.1.1-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.1-fix-baubles.patch deleted file mode 100644 index 2c5f659b8..000000000 --- a/sci-chemistry/ccp4i/files/6.1.1-fix-baubles.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 -+++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 -@@ -53,8 +53,8 @@ - RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" - RUN_CCP4MG _text "ccp4mg" - RUN_COOT _text "coot" --RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" --RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" -+RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" -+RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" - ENABLE_BUBBLE_HELP _logical 1 - DISABLE_TASKS _logical 1 - CCP4_SETUP_COMMAND _text setup_ccp4 -@@ -62,7 +62,7 @@ - BLT_LIBRARY _text "" - MENU_LENGTH _positiveint 25 - HYPERTEXT_VIEWER _text firefox --START_NETSCAPE _text netscape -+START_NETSCAPE _text firefox - O_MAPMAN _text mapman - MAPMAN_MAXSIZE _positiveint 4194304 - QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.1-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.1-rename-rapper.patch deleted file mode 100644 index a50ae6dbd..000000000 --- a/sci-chemistry/ccp4i/files/6.1.1-rename-rapper.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100 -+++ ccp4i/scripts/rapper.script.new 2009-03-12 23:34:47.000000000 +0100 -@@ -17,7 +17,7 @@ - - #set up command line - --set cmd "[BinPath rapper]" -+set cmd "[BinPath rappermc]" - - set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] - set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] - diff --git a/sci-chemistry/ccp4i/files/6.1.1-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.1-rename-superpose.patch deleted file mode 100644 index 90480eb8e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.1-rename-superpose.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script ---- ccp4-6.1.1/ccp4i/scripts/superpose.script 2006-07-26 16:22:49.000000000 +0200 -+++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script 2009-07-05 22:11:59.000000000 +0200 -@@ -21,7 +21,7 @@ - - if { [regexp SSM $SUPERPOSE_MODE ] } { - -- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" -+ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" - set status [Execute $cmd "" program_status report ] - - } elseif { [regexp TOP $SUPERPOSE_MODE ] } { diff --git a/sci-chemistry/ccp4i/files/6.1.1-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.1-rename-truncate.patch deleted file mode 100644 index 26f1cda3e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.1-rename-truncate.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ./ccp4i/templates/truncate.com.orig 2009-03-02 23:31:04.000000000 -0800 -+++ ./ccp4i/templates/truncate.com 2009-03-02 23:31:08.000000000 -0800 -@@ -11,7 +11,7 @@ - $SYMMETRY symmetry $SPACE_GROUP - $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6 - --1 truncate -+1 ftruncate - - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO - {[IfSet $ANOMALOUS]} anomalous - - $ANOMALOUS YES | NO ---- ./ccp4i/scripts/truncate.script.orig 2009-03-02 23:39:04.000000000 -0800 -+++ ./ccp4i/scripts/truncate.script 2009-03-02 23:39:41.000000000 -0800 -@@ -45,7 +45,7 @@ - - CreateComScript truncate truncate_script - -- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" - if { ![StringSame $INPUT_DATA AMPLITUDES] } { - append cmd " HKLOUT \"$HKL_TRUNCATE\"" - } diff --git a/sci-chemistry/ccp4i/files/6.1.2-crank_shelxd.tcl.patch b/sci-chemistry/ccp4i/files/6.1.2-crank_shelxd.tcl.patch deleted file mode 100644 index 0996065f3..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-crank_shelxd.tcl.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4i/crank/plugins/shelxd/crank_shelxd.tcl 2009-09-02 21:28:51.000000000 +0200 -+++ ccp4i/crank/plugins/shelxd/crank_shelxd.tcl 2009-08-17 21:17:55.000000000 +0200 -@@ -114,7 +114,7 @@ - puts $smalllog "Trial CCweak CC \$\$ \$\$" - for {set i 1} {$i <= $ntrial} {incr i} { - if { [info exists accweak($i)] && [info exists acc($i)] } { -- if { $accweak($i) > maxaccweak } { -+ if { $accweak($i) > $maxaccweak } { - set maxaccweak accweak($i) - set trialmaxaccweak $i - set maxacc acc($i) diff --git a/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch deleted file mode 100644 index 2c5f659b8..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-fix-baubles.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 -+++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 -@@ -53,8 +53,8 @@ - RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" - RUN_CCP4MG _text "ccp4mg" - RUN_COOT _text "coot" --RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" --RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" -+RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" -+RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" - ENABLE_BUBBLE_HELP _logical 1 - DISABLE_TASKS _logical 1 - CCP4_SETUP_COMMAND _text setup_ccp4 -@@ -62,7 +62,7 @@ - BLT_LIBRARY _text "" - MENU_LENGTH _positiveint 25 - HYPERTEXT_VIEWER _text firefox --START_NETSCAPE _text netscape -+START_NETSCAPE _text firefox - O_MAPMAN _text mapman - MAPMAN_MAXSIZE _positiveint 4194304 - QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.2-fix-f2mtz.patch b/sci-chemistry/ccp4i/files/6.1.2-fix-f2mtz.patch deleted file mode 100644 index 6296a1e36..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-fix-f2mtz.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/ccp4i/scripts/import.script -+++ b/ccp4i/scripts/import.script -@@ -188,6 +188,10 @@ END\n" - - set status [Execute $cmd $ctruncate_script program_status report ] - -+ # Copy the output mtz from Ctruncate to the tmpmtz variable so that it will become -+ # HKLOUT. Note that ctruncate carries over the I/SIGI columns by default. -+ -+ set tmpmtz $truncatemtz - } - - #===================================================================== diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch deleted file mode 100644 index a50ae6dbd..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-rename-rapper.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100 -+++ ccp4i/scripts/rapper.script.new 2009-03-12 23:34:47.000000000 +0100 -@@ -17,7 +17,7 @@ - - #set up command line - --set cmd "[BinPath rapper]" -+set cmd "[BinPath rappermc]" - - set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] - set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] - diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch deleted file mode 100644 index 90480eb8e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-rename-superpose.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script ---- ccp4-6.1.1/ccp4i/scripts/superpose.script 2006-07-26 16:22:49.000000000 +0200 -+++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script 2009-07-05 22:11:59.000000000 +0200 -@@ -21,7 +21,7 @@ - - if { [regexp SSM $SUPERPOSE_MODE ] } { - -- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" -+ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" - set status [Execute $cmd "" program_status report ] - - } elseif { [regexp TOP $SUPERPOSE_MODE ] } { diff --git a/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch deleted file mode 100644 index 26f1cda3e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.2-rename-truncate.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ./ccp4i/templates/truncate.com.orig 2009-03-02 23:31:04.000000000 -0800 -+++ ./ccp4i/templates/truncate.com 2009-03-02 23:31:08.000000000 -0800 -@@ -11,7 +11,7 @@ - $SYMMETRY symmetry $SPACE_GROUP - $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6 - --1 truncate -+1 ftruncate - - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO - {[IfSet $ANOMALOUS]} anomalous - - $ANOMALOUS YES | NO ---- ./ccp4i/scripts/truncate.script.orig 2009-03-02 23:39:04.000000000 -0800 -+++ ./ccp4i/scripts/truncate.script 2009-03-02 23:39:41.000000000 -0800 -@@ -45,7 +45,7 @@ - - CreateComScript truncate truncate_script - -- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" - if { ![StringSame $INPUT_DATA AMPLITUDES] } { - append cmd " HKLOUT \"$HKL_TRUNCATE\"" - } diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch deleted file mode 100644 index 2c5f659b8..000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 -+++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 -@@ -53,8 +53,8 @@ - RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" - RUN_CCP4MG _text "ccp4mg" - RUN_COOT _text "coot" --RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" --RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" -+RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" -+RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" - ENABLE_BUBBLE_HELP _logical 1 - DISABLE_TASKS _logical 1 - CCP4_SETUP_COMMAND _text setup_ccp4 -@@ -62,7 +62,7 @@ - BLT_LIBRARY _text "" - MENU_LENGTH _positiveint 25 - HYPERTEXT_VIEWER _text firefox --START_NETSCAPE _text netscape -+START_NETSCAPE _text firefox - O_MAPMAN _text mapman - MAPMAN_MAXSIZE _positiveint 4194304 - QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch deleted file mode 100644 index a50ae6dbd..000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- ccp4i/scripts/rapper.script 2009-02-03 11:49:50.000000000 +0100 -+++ ccp4i/scripts/rapper.script.new 2009-03-12 23:34:47.000000000 +0100 -@@ -17,7 +17,7 @@ - - #set up command line - --set cmd "[BinPath rapper]" -+set cmd "[BinPath rappermc]" - - set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] - set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] - diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch deleted file mode 100644 index 90480eb8e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -arNu ccp4-6.1.1/ccp4i/scripts/superpose.script ccp4-6.1.1.new/ccp4i/scripts/superpose.script ---- ccp4-6.1.1/ccp4i/scripts/superpose.script 2006-07-26 16:22:49.000000000 +0200 -+++ ccp4-6.1.1.new/ccp4i/scripts/superpose.script 2009-07-05 22:11:59.000000000 +0200 -@@ -21,7 +21,7 @@ - - if { [regexp SSM $SUPERPOSE_MODE ] } { - -- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" -+ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" - set status [Execute $cmd "" program_status report ] - - } elseif { [regexp TOP $SUPERPOSE_MODE ] } { diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch deleted file mode 100644 index 26f1cda3e..000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ./ccp4i/templates/truncate.com.orig 2009-03-02 23:31:04.000000000 -0800 -+++ ./ccp4i/templates/truncate.com 2009-03-02 23:31:08.000000000 -0800 -@@ -11,7 +11,7 @@ - $SYMMETRY symmetry $SPACE_GROUP - $CELL cell $CELL_1 $CELL_2 $CELL_3 $CELL_4 $CELL_5 $CELL_6 - --1 truncate -+1 ftruncate - - { [StringSame $APPLY_TRUNCATE "WILSON" ] } YES | NO - {[IfSet $ANOMALOUS]} anomalous - - $ANOMALOUS YES | NO ---- ./ccp4i/scripts/truncate.script.orig 2009-03-02 23:39:04.000000000 -0800 -+++ ./ccp4i/scripts/truncate.script 2009-03-02 23:39:41.000000000 -0800 -@@ -45,7 +45,7 @@ - - CreateComScript truncate truncate_script - -- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" - if { ![StringSame $INPUT_DATA AMPLITUDES] } { - append cmd " HKLOUT \"$HKL_TRUNCATE\"" - } diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml deleted file mode 100644 index 9ac9ffdb3..000000000 --- a/sci-chemistry/ccp4i/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-chemistry</herd> -</pkgmetadata> |