New features in WebMO version 7.0 include:

(Portage version: 2.1.2.5)

4 files changed, 180 insertions, 2 deletions

diff --git a/sci-chemistry/webmo/ChangeLog b/sci-chemistry/webmo/ChangeLog
index b92a13306e1b..ec03856c4d57 100644
--- a/sci-chemistry/webmo/ChangeLog
+++ b/sci-chemistry/webmo/ChangeLog
@@ -1,6 +1,19 @@
 # ChangeLog for sci-chemistry/webmo
-# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/ChangeLog,v 1.11 2006/09/20 05:08:59 dberkholz Exp $
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/ChangeLog,v 1.12 2007/05/08 06:43:35 dberkholz Exp $
+
+*webmo-7.0.003 (08 May 2007)
+
+  08 May 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/7.0.003-gentoo-locations.patch, +webmo-7.0.003.ebuild:
+  New features in WebMO version 7.0 include:
+    * Improved molecular mechanics for generating initial geometries
+    * Improved Editor clean-up for charged species and/or octet rule exceptions
+    * Automatic diagnosis and reporting of common causes of job failure
+    * JPEG image capture of molecular and spectral images
+    * Database storage of jobs and users for improved performance and scalability
+    * New administrative interface
+    * Many user interface enhancements and bug fixes
 
   20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
   (#148281) Change herd to sci-chemistry from sci.
diff --git a/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch b/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch
new file mode 100644
index 000000000000..1190c648a677
--- /dev/null
+++ b/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch
@@ -0,0 +1,42 @@
+diff -urN WebMO.install.orig/cgi-bin/interfaces/gamess.int.disabled WebMO.install/cgi-bin/interfaces/gamess.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/gamess.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/gamess.int.disabled	2007-05-07 23:32:19.000000000 -0700
+@@ -2,7 +2,7 @@
+ interfaceDescription{'gamess_admin'}="Edit preferences specific to Gamess"
+ interfaceDescription{'gamess_name'}="Gamess"
+ gamessVersion="2006"
+-gamessGMSPATH="/usr/local/gamess"
++gamessGMSPATH="/usr/bin"
+ gamessBinary="gamess.00.x"
+ gamessDdikick="ddikick.x"
+ cpuMin="0"
+diff -urN WebMO.install.orig/cgi-bin/interfaces/mopac.int.disabled WebMO.install/cgi-bin/interfaces/mopac.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/mopac.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/mopac.int.disabled	2007-05-07 23:31:43.000000000 -0700
+@@ -2,8 +2,8 @@
+ interfaceDescription{'mopac_admin'}="Edit preferences specific to Mopac"
+ interfaceDescription{'mopac_name'}="Mopac"
+ mopacVersion="7"
+-mopacPath="/usr/local/mopac7/mopac.exe"
+-mopacScratch="/scratch"
++mopacPath="/usr/bin/mopac7"
++mopacScratch="/tmp"
+ mopacExternal="/usr/local/mopac7"
+ cpuMin="0"
+ cpuMax="100"
+diff -urN WebMO.install.orig/cgi-bin/interfaces/tinker.int.disabled WebMO.install/cgi-bin/interfaces/tinker.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/tinker.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/tinker.int.disabled	2007-05-07 23:31:43.000000000 -0700
+@@ -2,9 +2,9 @@
+ interfaceDescription{'tinker_admin'}="Edit preferences specific to Tinker"
+ interfaceDescription{'tinker_name'}="Tinker"
+ tinkerVersion="4.2"
+-tinkerBinDir="/usr/local/tinker/bin"
+-tinkerBinExt="x"
+-tinkerParamDir="/usr/local/tinker/params"
++tinkerBinDir="/usr/bin"
++tinkerBinExt=""
++tinkerParamDir="/usr/share/tinker/params"
+ cpuMin="0"
+ cpuMax="100"
+ cpuDefault="100"
diff --git a/sci-chemistry/webmo/files/digest-webmo-7.0.003 b/sci-chemistry/webmo/files/digest-webmo-7.0.003
new file mode 100644
index 000000000000..2c74be1a7a43
--- /dev/null
+++ b/sci-chemistry/webmo/files/digest-webmo-7.0.003
@@ -0,0 +1,3 @@
+MD5 29d65a5b0182775ccd9f6e6c2d6fcef1 WebMO.7.0.003.tar.gz 1491250
+RMD160 42a73223370ad5e6e5b0baca95c9b3a1b01a8a09 WebMO.7.0.003.tar.gz 1491250
+SHA256 41018522a78f752bf07ad4ae6798c9eac0d678aba7d1f71f7c6dd5c4f00b2435 WebMO.7.0.003.tar.gz 1491250
diff --git a/sci-chemistry/webmo/webmo-7.0.003.ebuild b/sci-chemistry/webmo/webmo-7.0.003.ebuild
new file mode 100644
index 000000000000..0a884a3eddce
--- /dev/null
+++ b/sci-chemistry/webmo/webmo-7.0.003.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/webmo-7.0.003.ebuild,v 1.1 2007/05/08 06:43:35 dberkholz Exp $
+
+inherit eutils webapp
+
+MY_SRC_PN="WebMO"
+MY_SRC_P="${MY_SRC_PN}.${PV}"
+DESCRIPTION="Web-based interface to computational chemistry packages"
+HOMEPAGE="http://webmo.net/"
+SRC_URI="${MY_SRC_P}.tar.gz"
+LICENSE="WebMO"
+SLOT="${PVR}"
+KEYWORDS="~x86"
+RESTRICT="fetch"
+IUSE=""
+RDEPEND="dev-lang/perl
+	net-www/apache"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_SRC_PN}.install"
+
+pkg_nofetch() {
+	einfo "Go to http://webmo.net/ and register for a free license."
+	einfo "Download ${SRC_URI} and place it in ${DISTDIR}."
+}
+
+src_unpack() {
+	# We need a license number to proceed
+	if [[ -z ${WEBMO_LICENSE} ]]; then
+		msg="You must set WEBMO_LICENSE to your license number in make.conf."
+		ewarn "$msg"
+		die "$msg"
+	fi
+
+	# Check for invalid license values. Valid are dddd-dddd-dddd
+	if [[ ${WEBMO_LICENSE} != [0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9] ]]; then
+		msg="Invalid license format. Licenses should be DDDD-DDDD-DDDD (D is a digit)."
+		ewarn "$msg"
+		die "$msg"
+	fi
+
+	unpack ${A}
+
+	# Set up program locations to match where portage installs them
+	epatch ${FILESDIR}/${PV}-gentoo-locations.patch
+
+	# Add a data directory for gamess, because WebMO expects everything
+	# in one directory instead of FHS
+	# (Depends on gentoo-locations.patch)
+	epatch ${FILESDIR}/add-gamess-data-directory.patch
+
+	# Don't run diagnose.pl or ask about being root user
+	epatch ${FILESDIR}/dont-be-interactive-or-diagnose.patch
+
+	# Make setup.conf
+	create_setup_conf
+}
+
+src_install() {
+	webapp_src_preinst
+
+	# Install everything
+	perl setup.pl || die "Check ${S}/diagnose.html for errors"
+
+	# Get ${D} out of main config file
+	dosed "${MY_CGIBINDIR}/webmo/interfaces/globals.int"
+
+	webapp_hook_script ${FILESDIR}/reconfig
+
+	local files=$(find ${D}${MY_HOSTROOTDIR}/webmo ${D}${MY_CGIBINDIR}/webmo/interfaces)
+	# Add the directories themselves
+	files="${files} ${MY_HOSTROOTDIR}/webmo ${MY_CGIBINDIR}/webmo/interfaces"
+	files=${files//${D}/}
+	for file in ${files}; do
+		webapp_configfile "${file}"
+		webapp_serverowned "${file}"
+	done
+
+	ebegin "Fixing permissions"
+	pushd "${D}" > /dev/null
+	find . -perm /o+w -type f | xargs fperms 664
+	find . -perm /o+w -type d | xargs fperms 775
+	popd > /dev/null
+	eend 0
+
+	webapp_src_install
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Be sure that this line is uncommented in httpd.conf:"
+	einfo "AddHandle cgi-scripts .cgi"
+	einfo
+	einfo "The diagnose.pl script can be run if WebMO doesn't work properly."
+	einfo
+	ewarn "Be careful never to overwrite your user, group or job databases"
+	ewarn "when using etc-update after an upgrade."
+
+	webapp_pkg_postinst
+}
+
+create_setup_conf() {
+	local SETUP_CONF="${S}/setup.conf"
+
+	echo_setup perlPath /usr/bin/perl "${SETUP_CONF}"
+	echo_setup htmlBase "${D}${MY_HTDOCSDIR}" "${SETUP_CONF}"
+	echo_setup url_htmlBase /webmo "${SETUP_CONF}"
+	echo_setup cgiBase "${D}${MY_CGIBINDIR}/webmo" "${SETUP_CONF}"
+	echo_setup url_cgiBase /cgi-bin/webmo "${SETUP_CONF}"
+	echo_setup userBase "${D}${MY_HOSTROOTDIR}/webmo" "${SETUP_CONF}"
+	echo_setup license "${WEBMO_LICENSE}" "${SETUP_CONF}"
+}
+
+# Takes three arguments:
+# 1: variable, 2: value, 3: file to echo them to
+echo_setup() {
+	# All values must be double-quoted, so escape the inner quotes.
+	echo "${1}=\"${2}\"" >> ${3}
+}