Splitted interface from ccp4

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

8 files changed, 184 insertions, 0 deletions

diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog
new file mode 100644
index 000000000000..698351279345
--- /dev/null
+++ b/sci-chemistry/ccp4i/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/ccp4i
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ChangeLog,v 1.1 2010/02/06 00:24:33 jlec Exp $
+
+*ccp4i-6.1.3 (06 Feb 2010)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/6.1.3-fix-baubles.patch, +files/6.1.3-rename-rapper.patch,
+  +files/6.1.3-rename-superpose.patch, +files/6.1.3-rename-truncate.patch,
+  +ccp4i-6.1.3.ebuild, +metadata.xml:
+  Interface splitted from ccp4
+
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
new file mode 100644
index 000000000000..1cc2ccdae62b
--- /dev/null
+++ b/sci-chemistry/ccp4i/Manifest
@@ -0,0 +1,19 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 6.1.3-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934 SHA1 cdc8752026f3cdd96ee0fd6a3f558e0729f88a6a SHA256 37c217f339a46a6b830ce8e791cbd32655e31ab8d58267fb625e841e867402b4
+AUX 6.1.3-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728
+AUX 6.1.3-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
+AUX 6.1.3-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
+DIST 6.1.3-oasis4.0.patch.bz2 946 RMD160 b448376114ba41e6999d533929fdb79812476f87 SHA1 7667aca14d28cec01bfa7d2eee9cbce11624f4fa SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b
+DIST ccp4-6.1.3-core-src.tar.gz 242109897 RMD160 babe577296d19849de095d5716d4e18ac3e8a4b5 SHA1 0d5d69f66b9ae24c66e767e8493d562e50962f75 SHA256 e57cdd193e2a80a0ce94b76fa6d658b111872a9c4800b942edf585f4defcc4fe
+EBUILD ccp4i-6.1.3.ebuild 1896 RMD160 3b8c19bab9c7e4099aad28e24e091d9ee56eeb5e SHA1 d763e0a7a7ebdbc89876a2aff3e6bffdbe2e4c17 SHA256 dffa32057d1dd0d49bebc26a5714e466c450d4d35377e906925e7e37267a0361
+MISC ChangeLog 504 RMD160 b9a8163d39d83a2b5714b84f101d2f674c97c98e SHA1 d88a49981456daaa0b1c513b18cd457a71ef1a94 SHA256 45325a69436e9b2c61572ad0ec9f8f4a8a0519462cd6619df846deaf675b3937
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAktstsUACgkQgAnW8HDreRZEjACcCRypwddGQ1fQkW/IZfJHJ7F2
+oPcAoJjqIGMqCnEI7uvkHd1AnJ7gdKGJ
+=2a7R
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild
new file mode 100644
index 000000000000..f01df13f6e02
--- /dev/null
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild,v 1.1 2010/02/06 00:24:33 jlec Exp $
+
+EAPI="2"
+
+inherit base multilib
+
+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=""
+
+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/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
new file mode 100644
index 000000000000..2c5f659b8018
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
@@ -0,0 +1,22 @@
+--- 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
new file mode 100644
index 000000000000..a50ae6dbd648
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
@@ -0,0 +1,12 @@
+--- 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
new file mode 100644
index 000000000000..90480eb8e381
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 000000000000..26f1cda3e381
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
@@ -0,0 +1,22 @@
+--- ./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
new file mode 100644
index 000000000000..9ac9ffdb3a41
--- /dev/null
+++ b/sci-chemistry/ccp4i/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+</pkgmetadata>