Splitted xia from ccp4

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

5 files changed, 153 insertions, 0 deletions

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
new file mode 100644
index 000000000000..efa260c601ff
--- /dev/null
+++ b/sci-chemistry/xia2/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/xia2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.1 2010/02/06 23:36:47 jlec Exp $
+
+*xia2-0.3.1.0 (06 Feb 2010)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/0.3.1.0-fix-syntax.patch, +xia2-0.3.1.0.ebuild, +metadata.xml:
+  Splitted xia2 from ccp4
+
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
new file mode 100644
index 000000000000..4e5d1743d2f5
--- /dev/null
+++ b/sci-chemistry/xia2/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 0.3.1.0-fix-syntax.patch 2586 RMD160 23e70c32e9052ff3a12740b71a02a66a5053b8da SHA1 3fdcad17357908ac923a87c9e93364e92b35190f SHA256 4e95f9e9f26d8b4400481b2542ad9e1ca2adaafb6caedb5c57d149f4e2554285
+DIST xia2-0.3.1.0.tar.bz2 3389906 RMD160 da2b84535e418c266c316a6fce40dd57b1fb6adc SHA1 ded8f83026af9d44053cb17c91fc6130d63d6777 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28
+EBUILD xia2-0.3.1.0.ebuild 1470 RMD160 b97c2b93826b4cf467c34a1924ad53e59b5af43b SHA1 b042d3ef02d9bb916d6edc0dc7dabd4947a5e534 SHA256 ebd563e52c5e9be399f0e2a88f94581db5f4fd9e385d3521fc269b6335bcf63c
+MISC ChangeLog 389 RMD160 ce5796c19e5d19265d0c063fab5e92f08224d7d8 SHA1 aa0dcba1b10ef5954dfb319ae860f867dfeed095 SHA256 de76c7207762de60a4d9adbca84673ef68c050dbdaa489ea0a132e2184d3340c
+MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAktt/RUACgkQgAnW8HDreRYSOwCgnIi4gRErLhzfkXFGoV4I0uB4
+OGUAn1TAFqd6ZwyAZq/PU99daAWVTDF0
+=LuGX
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
new file mode 100644
index 000000000000..9d92af7e33ce
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
@@ -0,0 +1,61 @@
+diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py
+index 1a3b0e2..e0b8a1e 100755
+--- a/xia2-0.3.1.0/Applications/xia2find.py
++++ b/xia2-0.3.1.0/Applications/xia2find.py
+@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
+ from Experts.FindImages import image2template_directory
+ 
+ known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
+-                          'osc', 'cbf', 'mar2000']]
++                          'osc', 'cbf', 'mar2000']
+ known_sweeps = { }
+ 
+ def is_image_name(file):
+diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
+index 28b1dc3..dba3ef7 100644
+--- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py
++++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
+@@ -48,24 +48,24 @@ strategy_dict = {
+     'default':{
+     'score':1,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
++    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
+     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
+                   'pointless-1.1.0.4']},
+     'default':{
+     'score':2,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
++    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
+     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
+                   'pointless-1.1.0.4']},
+     'mosaic':{
+     'score':1,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
++    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
+     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
+                   'pointless-1.1.0.4']},
+     'mosaic':{
+     'score':2,
+     'pipeline':{
+-    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
++    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
+     'depends-on':['xds', 'xscale']}
+     }
+diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
++++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
+@@ -49,8 +49,8 @@ def Cad(DriverType = None):
+             self.add_command_line(hklin)
+ 
+             self.set_task('Rewriting reflections %s => %s' % 
+-                      `   (os.path.split(hklin)[-1],
+-                       `   os.path.split(self.getHklout())[-1]))
++                         (os.path.split(hklin)[-1],
++                          os.path.split(self.getHklout())[-1]))
+ 
+             self.start()
+ 
diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml
new file mode 100644
index 000000000000..efb490d78817
--- /dev/null
+++ b/sci-chemistry/xia2/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>sci@gentoo.org</email>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
new file mode 100644
index 000000000000..276c76ae4ffa
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.0.ebuild,v 1.1 2010/02/06 23:36:47 jlec Exp $
+
+EAPI="3"
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.xia2.org/xia/"
+SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	>=sci-chemistry/ccp4-apps-6.1.2
+	sci-chemistry/mosflm
+	sci-chemistry/pointless
+	>=sci-libs/ccp4-libs-6.1.2
+	sci-libs/cctbx"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	find . -name '*.bat' | xargs rm || die
+
+	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
+}
+
+src_install() {
+	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
+
+	insinto /usr/share/ccp4/XIAROOT/
+	doins -r * || die
+
+	# Set programs executable
+# fperms cannot handle wildcards
+	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
+	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
+
+	cat >> "${T}"/23XIA <<- EOF
+	XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
+	XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
+	XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
+	PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
+	EOF
+
+	doenvd "${T}"/23XIA
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/share/ccp4/XIAROOT
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/share/ccp4/XIAROOT
+}