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authorJustin Lecher (jlec) <jlec@j-schmitz.net>2009-12-22 23:21:20 +0100
committerJustin Lecher (jlec) <jlec@j-schmitz.net>2009-12-22 23:21:20 +0100
commit39042d0d04904784f6e39fc7c8fdf93db2f077e2 (patch)
tree65cf63cfd1ad6592cb6b93f29f033610adaa0357
parentsci-libs/ccp4-libs -- Version bump (diff)
downloadsci-39042d0d04904784f6e39fc7c8fdf93db2f077e2.tar.gz
sci-39042d0d04904784f6e39fc7c8fdf93db2f077e2.tar.bz2
sci-39042d0d04904784f6e39fc7c8fdf93db2f077e2.zip
sci-chemistry/ccp4i -- Version bump
(Portage version: 2.2_rc60/git/Linux x86_64) (Signed Manifest commit)
-rw-r--r--sci-chemistry/ccp4i/ChangeLog8
-rw-r--r--sci-chemistry/ccp4i/Manifest15
-rw-r--r--sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild82
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch22
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch12
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch12
-rw-r--r--sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch22
7 files changed, 169 insertions, 4 deletions
diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog
index 61b10c121..d7e9bace8 100644
--- a/sci-chemistry/ccp4i/ChangeLog
+++ b/sci-chemistry/ccp4i/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*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>
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
index dbf51f1c2..612daafd5 100644
--- a/sci-chemistry/ccp4i/Manifest
+++ b/sci-chemistry/ccp4i/Manifest
@@ -11,21 +11,28 @@ AUX 6.1.2-fix-f2mtz.patch 467 RMD160 5a277a96adf00b19da6811141fc41d736d57354d SH
AUX 6.1.2-rename-rapper.patch 380 RMD160 e8306cec04348a56fbe00026333b27ce2a8544f8 SHA1 f5a87898394add359a1e6f6ceb837530dc53646f SHA256 e15407959e565d32874d2db9003168559b7e9b14f0e68207560d4a5b4db8a728
AUX 6.1.2-rename-superpose.patch 655 RMD160 6647dc3e0a021f9809d74d5dd785dd6bde456c22 SHA1 485a2e3cd46864769c6cfe10b9b0224ca896d2d6 SHA256 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
AUX 6.1.2-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
+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 6.1.1-090511-updates.patch.bz2 8915 RMD160 58114b0ba6d225078044a8a6f9245aab66c6b572 SHA1 15c327c0b218b542b0c3955a9e63d2c6de299f7e SHA256 c0dbbde05b72f2460ada22f556d4cfe1f286a448ceb1181fd48b758468e509ac
DIST 6.1.2-oasis4.0.patch.bz2 36289 RMD160 9e08cae9250469bef1ba91833f4e9a782092e9d2 SHA1 1f6853711a781179f02bb6b1ce97c56bcda3d824 SHA256 a49c62f9a5971bfc5abefbd4b93df5819c3720e0d46954af52cd28c71653110b
+DIST 6.1.3-oasis4.0.patch.bz2 946 RMD160 b448376114ba41e6999d533929fdb79812476f87 SHA1 7667aca14d28cec01bfa7d2eee9cbce11624f4fa SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b
DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
DIST ccp4-6.1.1-src-patch-04_03_09.tar.gz 279642 RMD160 1a7c3b6cc846d315fc577e78b4aa00ab85a3d3d2 SHA1 29dbb84f3d63fc860694473ca99cf8bb71dae18a SHA256 eb806168235b55fbafdd72591ba94d35b78cc715a56a8b90979644d420ad672a
DIST ccp4-6.1.2-core-src.tar.gz 247203188 RMD160 19019c6cd37e83cf6d2d19f91979edc978d18395 SHA1 2423178d3877dd44d3671a7eb4d6666de6852cb7 SHA256 bcae870675270be410278d9a6f2ee19f9caf32b73fd969e9381a4d510f174c75
+DIST ccp4-6.1.3-core-src.tar.gz 241654695 RMD160 922e723521a94b787f187e714704fce6d705fc5e SHA1 6fc20a2c5956f8640267733dd419a863213bbfc1 SHA256 c76ddeecacfb396416f6e067f0b21532c1376dfc34dcaaa4edc89389cd20f8eb
EBUILD ccp4i-6.1.1-r5.ebuild 1444 RMD160 c69583b66d51e059ef2ba00c304c7830d32bfebf SHA1 6a590ca81abdb2d41a6131d257595f01e2799da7 SHA256 44a1124ee6797fc66030ce4610655bfd4c74d451add4dd865f9806bde422c19b
EBUILD ccp4i-6.1.2-r4.ebuild 1843 RMD160 40338ac92e710ff1679436f4688eb046eb6fa980 SHA1 ee397bbaa02011fc0e966ee2c46a4eaebd1d01a5 SHA256 0be9912ae414cd549b44f46788c8eee1f80fa99d4860018cd93732d428c899dc
EBUILD ccp4i-6.1.2-r5.ebuild 1880 RMD160 346ddf9eccdb66259f2ab39d9b66f0652a010a7c SHA1 804f038e35ae79e8d58f23020d713bb9bdd534d1 SHA256 b559644171a1e0c2fb77e857e53907844efc43d9d78e089e7eebc4f2f22d1e14
EBUILD ccp4i-6.1.2-r7.ebuild 2003 RMD160 8de16c2d3e982980b595fe300ec1507e7ff30d2f SHA1 23cd09ca792fd7a2c64005234ee7c790cfc51e1f SHA256 5966b4c9daea1c2da963a7911676c999b6679b8982480c9031f9c800b591b62c
-MISC ChangeLog 3443 RMD160 0f7ed267a3aad3c8c1ecb6feb730de1f83e2f128 SHA1 8c29576de39fa2060c60d35885cb686f08a654bb SHA256 7cc918e9b027eadd792862b756204c3c480a1208d7b187d74ba0010d12dcb57a
+EBUILD ccp4i-6.1.3.ebuild 1817 RMD160 40b4e5c6dd599787e735ec63a0240ed410775615 SHA1 2947df11574b779f19dd4d1af122765b0c0045c3 SHA256 72abbb7611398a3495f96fb6c5c0967117653c95f4342cd18325f4a9bc3d7699
+MISC ChangeLog 3710 RMD160 c9e7346691b09fe278e8e5a84fc3d06e885125c3 SHA1 3291c9eb3c651fd821014e915bf37396b4ae2880 SHA256 f908b02b268ab06c86f22e8a6611d503e3907bf0deb242606144b0fb485b0241
MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.11 (GNU/Linux)
-iEYEARECAAYFAksNCI4ACgkQgAnW8HDreRYUeQCfXSLsss9UX7ZT3MXsxC1dpnm4
-wwgAoLkggmHEUv1+T/z0OPnsEVWoivff
-=oIFp
+iEYEARECAAYFAksxRl8ACgkQgAnW8HDreRa+2QCfeDBeHrLp8rbz8wRjKsOaRuEs
+2ncAnRRWPRadc1b7SKA73t9qOZ8oBnUn
+=kYt8
-----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 000000000..d0ba8ef17
--- /dev/null
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.3.ebuild
@@ -0,0 +1,82 @@
+# 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}"/${PV}-rename-truncate.patch
+ "${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 000000000..2c5f659b8
--- /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 000000000..a50ae6dbd
--- /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 000000000..90480eb8e
--- /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 000000000..26f1cda3e
--- /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\""
+ }