sci-chemistry/ccp4i

fix for f2mtz
bug 289379

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(Portage version: 2.2_rc48/git/Linux x86_64)
 (Signed Manifest commit)

4 files changed, 117 insertions, 1 deletions

diff --git a/sci-chemistry/ccp4i/ChangeLog b/sci-chemistry/ccp4i/ChangeLog
index e7d9cd861..d34c2f195 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-6.1.2-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>
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
index b42b582eb..15e40ed1a 100644
--- a/sci-chemistry/ccp4i/Manifest
+++ b/sci-chemistry/ccp4i/Manifest
@@ -1,9 +1,13 @@
+-----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 75791921692a603baa88dfa45ff48331ea8b6985a63f04a15ad43dd5be93e52e
 AUX 6.1.1-rename-truncate.patch 810 RMD160 33f8cb14a3bc0f9c6cd249df07f469c9d6601e4d SHA1 ac13f02b6141802e3762efe50a3d270169da0a54 SHA256 5a298cce47726d78ece397affdf1f2d550be520565c7dc5b47a953ab01d23ccd
 AUX 6.1.2-crank_shelxd.tcl.patch 539 RMD160 af90e7dc6c0437aac52a2ac734dac443d6866b5b SHA1 f121631ae38930f30be729807bc9c57c727015b7 SHA256 99a2108c8eec3e25e750f912d1d30a45a376fc9fc3bc5f3f1fa230b6ec5056ce
 AUX 6.1.2-fix-baubles.patch 1542 RMD160 c952d16d1e009a9ff345393494bf198fff997934 SHA1 cdc8752026f3cdd96ee0fd6a3f558e0729f88a6a SHA256 37c217f339a46a6b830ce8e791cbd32655e31ab8d58267fb625e841e867402b4
+AUX 6.1.2-fix-f2mtz.patch 467 RMD160 5a277a96adf00b19da6811141fc41d736d57354d SHA1 f20416d9aabad988b81e61723de86f8586bc824d SHA256 e10b30d80c6507c8a18a3a6d1e18bc211356e4670f03847b33f96264b48ab49b
 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
@@ -13,5 +17,13 @@ DIST ccp4-6.1.1-src-patch-04_03_09.tar.gz 279642 RMD160 1a7c3b6cc846d315fc577e78
 DIST ccp4-6.1.2-core-src.tar.gz 247203188 RMD160 19019c6cd37e83cf6d2d19f91979edc978d18395 SHA1 2423178d3877dd44d3671a7eb4d6666de6852cb7 SHA256 bcae870675270be410278d9a6f2ee19f9caf32b73fd969e9381a4d510f174c75
 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
-MISC ChangeLog 2842 RMD160 3c5b9c4fc7beaa3633886243656e107c9ce59b5b SHA1 7359aefc2f89a329f6ef0a6122a2801cc44648c7 SHA256 93eb601d27e03e4c3662b26a3b5d0f2b13e74ebd3cbec9cd5b62a5c704794b6c
+EBUILD ccp4i-6.1.2-r5.ebuild 1880 RMD160 346ddf9eccdb66259f2ab39d9b66f0652a010a7c SHA1 804f038e35ae79e8d58f23020d713bb9bdd534d1 SHA256 b559644171a1e0c2fb77e857e53907844efc43d9d78e089e7eebc4f2f22d1e14
+MISC ChangeLog 3032 RMD160 e93260407905a36b3d4951c7674f455ce4c53eaa SHA1 8e5574b8ae9b4ee9884ecb2ec7bfec0821e9f5b3 SHA256 88b707d16d75fdae4f9a5ebe6eb54811bf134adbcefe4f723a7876b83f62be2b
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkrvTT0ACgkQgAnW8HDreRYJCgCfZWD8Z4m/LGC+E/lJJXKS5zjB
+//8AnRCbquQOKJ2QifcrxGhb+IBpYK+B
+=MnLm
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild
new file mode 100644
index 000000000..6fce8ba71
--- /dev/null
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.2-r5.ebuild
@@ -0,0 +1,83 @@
+# 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/files/6.1.2-fix-f2mtz.patch b/sci-chemistry/ccp4i/files/6.1.2-fix-f2mtz.patch
new file mode 100644
index 000000000..6296a1e36
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.2-fix-f2mtz.patch
@@ -0,0 +1,13 @@
+--- 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
+   }
+ 
+ #=====================================================================