Add a Web interface to a number of computational chemistry programs. Ones in portage include mopac7, gamess and tinker. Also works for Gaussian, NWChem, QChem, Molpro, etc. What needs work: reinstallations without screwing the old configuration, and the reconfig script so editing globals.int isn't required.

(Portage version: 2.0.53)

9 files changed, 401 insertions, 0 deletions

diff --git a/sci-chemistry/webmo/ChangeLog b/sci-chemistry/webmo/ChangeLog
new file mode 100644
index 000000000000..1b038d44cb30
--- /dev/null
+++ b/sci-chemistry/webmo/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-chemistry/webmo
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/ChangeLog,v 1.1 2005/12/04 08:27:33 spyderous Exp $
+
+*webmo-6.0.003 (04 Dec 2005)
+
+  04 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/add-gamess-data-directory.patch,
+  +files/dont-be-interactive-if-root.patch,
+  +files/dont-check-unneeded-things.patch, +files/gentoo-locations.patch,
+  +metadata.xml, +webmo-6.0.003.ebuild:
+  Add a Web interface to a number of computational chemistry programs. Ones in
+  portage include mopac7, gamess and tinker. Also works for Gaussian, NWChem,
+  QChem, Molpro, etc. What needs work: reinstallations without screwing the
+  old configuration, and the reconfig script so editing globals.int isn't
+  required.
+
diff --git a/sci-chemistry/webmo/Manifest b/sci-chemistry/webmo/Manifest
new file mode 100644
index 000000000000..cffc2d867982
--- /dev/null
+++ b/sci-chemistry/webmo/Manifest
@@ -0,0 +1,8 @@
+MD5 8e94349e3989b4b0219b8b5d8616ff4a files/add-gamess-data-directory.patch 2112
+MD5 ea0135b660aec5e5627dd9929a937a41 files/digest-webmo-6.0.003 66
+MD5 b796d945112067cc23afa05e1c0f7463 files/dont-be-interactive-if-root.patch 1851
+MD5 ebcb1f46115574118ae40fc9fd01023d files/dont-check-unneeded-things.patch 3577
+MD5 c3f7daf2719dca6df3f68a7193213e63 files/gentoo-locations.patch 1939
+MD5 9922421ed5b1825187078d2466f0994a files/reconfig 617
+MD5 baccb961693e808c176bbe3e2d865af1 files/setup.conf 213
+MD5 9b2350b125e1a36d4752af77ab327447 webmo-6.0.003.ebuild 3269
diff --git a/sci-chemistry/webmo/files/add-gamess-data-directory.patch b/sci-chemistry/webmo/files/add-gamess-data-directory.patch
new file mode 100644
index 000000000000..9120a5c89e1e
--- /dev/null
+++ b/sci-chemistry/webmo/files/add-gamess-data-directory.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	2005-12-03 14:58:39.000000000 -0800
++++ WebMO.install/cgi-bin/interfaces/gamess.int.disabled	2005-12-03 14:58:59.000000000 -0800
+@@ -3,6 +3,7 @@
+ interfaceDescription{'gamess_name'}="Gamess"
+ gamessVersion="Unknown"
+ gamessGMSPATH="/usr/bin"
++gamessDATAPATH="/usr/share/gamess/ericfmt"
+ gamessBinary="gamess.00.x"
+ gamessDdikick="ddikick.x"
+ cpuMin="0"
+diff -urN WebMO.install.orig/cgi-bin/run_gamess.cgi WebMO.install/cgi-bin/run_gamess.cgi
+--- WebMO.install.orig/cgi-bin/run_gamess.cgi	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/cgi-bin/run_gamess.cgi	2005-12-03 14:54:54.000000000 -0800
+@@ -30,7 +30,7 @@
+ $ENV{'IRCDATA'} = $output_file.".irc";
+ $ENV{'PUNCH'} = $output_file.".dat";
+ $ENV{'INPUT'} = "$input_file.inp";
+-$ENV{'ERICFMT'} = "$gamessGMSPATH/ericfmt.dat";
++$ENV{'ERICFMT'} = "$gamessDATAPATH/ericfmt.dat";
+ $ENV{'PATH'} = $ENV{'PATH'}.":".$gamessGMSPATH;
+ 
+ # if we are using PBS, find out which host we are running on
+diff -urN WebMO.install.orig/source/gamessmgr_admin.html WebMO.install/source/gamessmgr_admin.html
+--- WebMO.install.orig/source/gamessmgr_admin.html	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/source/gamessmgr_admin.html	2005-12-03 14:55:00.000000000 -0800
+@@ -30,10 +30,14 @@
+ 							<TD><INPUT TYPE="text" NAME="gamessVersion" VALUE="<PERL>$gamessVersion</PERL>" SIZE=50></TD>
+ 						</TR>
+ 						<TR>
+-							<TD><B>Gamess directory</B></TD>
++							<TD><B>Gamess binary directory</B></TD>
+ 							<TD><INPUT TYPE="text" NAME="gamessGMSPATH" VALUE="<PERL>$gamessGMSPATH</PERL>" SIZE=50></TD>
+ 						</TR>
+ 						<TR>
++							<TD><B>Gamess data directory (ericfmt)</B></TD>
++							<TD><INPUT TYPE="text" NAME="gamessDATAPATH" VALUE="<PERL>$gamessDATAPATH</PERL>" SIZE=50></TD>
++						</TR>
++						<TR>
+ 							<TD><B>Gamess binary (name, not path)</B></TD>
+ 							<TD><INPUT TYPE="text" NAME="gamessBinary" VALUE="<PERL>$gamessBinary</PERL>" SIZE=50></TD>
+ 						</TR>
diff --git a/sci-chemistry/webmo/files/digest-webmo-6.0.003 b/sci-chemistry/webmo/files/digest-webmo-6.0.003
new file mode 100644
index 000000000000..3dffc03ca534
--- /dev/null
+++ b/sci-chemistry/webmo/files/digest-webmo-6.0.003
@@ -0,0 +1 @@
+MD5 8e19ca928fbc9128513b01f9e82bfcd6 WebMO.6.0.003.tar.gz 1197672
diff --git a/sci-chemistry/webmo/files/dont-be-interactive-if-root.patch b/sci-chemistry/webmo/files/dont-be-interactive-if-root.patch
new file mode 100644
index 000000000000..fdc7691cae88
--- /dev/null
+++ b/sci-chemistry/webmo/files/dont-be-interactive-if-root.patch
@@ -0,0 +1,49 @@
+--- WebMO.install.orig/setup.pl	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/setup.pl	2005-12-03 11:39:51.000000000 -0800
+@@ -82,26 +84,26 @@
+ #get a username
+ my $username = `whoami`; chomp $username;
+ my $homedir = $ENV{'HOME'} ne "" ? $ENV{'HOME'} : `echo ~`; chomp $homedir;
+-if ($username eq "root")
+-{
+-	print <<END;
+-	
+-You are installing WebMO as the user 'root'.  It is strongly suggested that
+-you do not install WebMO as 'root', but rather do one of the following:
+-  1) Create a new 'webmo'account; log into this account, and install WebMO
+-     into the 'webmo' home directory
+-  2) Log into an existing user acconut, and install WebMO into the home 
+-     directory
+-  3) Continue installation as 'root', but install WebMO into your system
+-     wide html/cgi-bin directory (do not install into a user home directory
+-     as 'root', as the cgi scripts may not run correctly)
+-     
+-END
+-	print "Do you wish to continue with setup?";
+-	my $choice = <STDIN>;
+-	chomp $choice;
+-	exit (0) unless ($choice =~ /^y/i);
+-}
++#if ($username eq "root")
++#{
++#	print <<END;
++#	
++#You are installing WebMO as the user 'root'.  It is strongly suggested that
++#you do not install WebMO as 'root', but rather do one of the following:
++#  1) Create a new 'webmo'account; log into this account, and install WebMO
++#     into the 'webmo' home directory
++#  2) Log into an existing user acconut, and install WebMO into the home 
++#     directory
++#  3) Continue installation as 'root', but install WebMO into your system
++#     wide html/cgi-bin directory (do not install into a user home directory
++#     as 'root', as the cgi scripts may not run correctly)
++#     
++#END
++#	print "Do you wish to continue with setup?";
++#	my $choice = <STDIN>;
++#	chomp $choice;
++#	exit (0) unless ($choice =~ /^y/i);
++#}
+ 
+ #get license information
+ &divider;
diff --git a/sci-chemistry/webmo/files/dont-check-unneeded-things.patch b/sci-chemistry/webmo/files/dont-check-unneeded-things.patch
new file mode 100644
index 000000000000..ad62f8021ce7
--- /dev/null
+++ b/sci-chemistry/webmo/files/dont-check-unneeded-things.patch
@@ -0,0 +1,114 @@
+--- WebMO.install.orig/scripts/diagnose.pl	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/scripts/diagnose.pl	2005-12-03 18:52:58.000000000 -0800
+@@ -80,26 +80,26 @@
+ print handle "\n";
+ 
+ # Check home directory
+-if ($ENV{'HOME'} ne "")
+-{
+-	print handle "<H3>Checking Home Directory</H3>";
+-	my $stat_info = stat($ENV{'HOME'});
+-	my $leng = length($ENV{'HOME'});
+-
+-	print handle "Checking home directory:";
+-	if (($stat_info->mode & 00001) != 1)
+-	{
+-		print handle "&nbsp;" x (59 - $leng);
+-		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
+-		printf handle "<B>Home directory must be world-executable if WebMO is installed there</B>\n"
+-	}
+-	else
+-	{
+-		print handle "&nbsp;" x (59 - $leng);
+-		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
+-	}
+-	print handle "\n";
+-}
++#if ($ENV{'HOME'} ne "")
++#{
++#	print handle "<H3>Checking Home Directory</H3>";
++#	my $stat_info = stat($ENV{'HOME'});
++#	my $leng = length($ENV{'HOME'});
++#
++#	print handle "Checking home directory:";
++#	if (($stat_info->mode & 00001) != 1)
++#	{
++#		print handle "&nbsp;" x (59 - $leng);
++#		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
++#		printf handle "<B>Home directory must be world-executable if WebMO is installed there</B>\n"
++#	}
++#	else
++#	{
++#		print handle "&nbsp;" x (59 - $leng);
++#		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
++#	}
++#	print handle "\n";
++#}
+ 
+ # Check permissions
+ print handle "<H3>Checking CGI Directory</H3>";
+@@ -345,36 +345,36 @@
+ 	}
+ 	
+ 	# check for AddHandler for cgi scripts	
+-	print  handle ($text = "Checking for AddHandler cgi-scripts enabled: ");
+-	$len = length($text);
+-	@results = grep(/AddHandler cgi\-script/, @contents);
+-	if ($results[0] =~ /^#/)
+-	{
+-		print handle "&nbsp;" x (70 - $len);
+-		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
+-		print handle "<B>Uncomment the line 'AddHandle cgi-scripts .cgi'</B>\n";
+-	}
+-	else
+-	{
+-		print handle "&nbsp;" x (70 - $len);
+-		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
+-	}
++#	print  handle ($text = "Checking for AddHandler cgi-scripts enabled: ");
++#	$len = length($text);
++#	@results = grep(/AddHandler cgi\-script/, @contents);
++#	if ($results[0] =~ /^#/)
++#	{
++#		print handle "&nbsp;" x (70 - $len);
++#		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
++#		print handle "<B>Uncomment the line 'AddHandle cgi-scripts .cgi'</B>\n";
++#	}
++#	else
++#	{
++#		print handle "&nbsp;" x (70 - $len);
++#		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
++#	}
+ 	
+ 	# check for user directories
+-	print  handle ($text = "Checking for UserDir enabled: ");
+-	$len = length($text);
+-	@results = grep(/UserDir /, @contents);
+-	if ($results[0] =~ /^#/)
+-	{
+-		print handle "&nbsp;" x (70 - $len);
+-		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
+-		print handle "<B>Uncomment the line 'UserDir public_html'</B>\n";
+-	}
+-	else
+-	{
+-		print handle "&nbsp;" x (70 - $len);
+-		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
+-	}
++#	print  handle ($text = "Checking for UserDir enabled: ");
++#	$len = length($text);
++#	@results = grep(/UserDir /, @contents);
++#	if ($results[0] =~ /^#/)
++#	{
++#		print handle "&nbsp;" x (70 - $len);
++#		print handle "<FONT COLOR=\"red\"><B>Failed</B></FONT>\n";
++#		print handle "<B>Uncomment the line 'UserDir public_html'</B>\n";
++#	}
++#	else
++#	{
++#		print handle "&nbsp;" x (70 - $len);
++#		print handle "<FONT COLOR=\"green\"><B>Passed</B></FONT>\n";
++#	}
+ 	
+ 	# check for suexec
+ 	print  handle ($text = "Checking for suExec enabled: ");
diff --git a/sci-chemistry/webmo/files/gentoo-locations.patch b/sci-chemistry/webmo/files/gentoo-locations.patch
new file mode 100644
index 000000000000..6bff53af4579
--- /dev/null
+++ b/sci-chemistry/webmo/files/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	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/cgi-bin/interfaces/gamess.int.disabled	2005-12-03 14:56:09.000000000 -0800
+@@ -2,7 +2,7 @@
+ interfaceDescription{'gamess_admin'}="Edit preferences specific to Gamess"
+ interfaceDescription{'gamess_name'}="Gamess"
+ gamessVersion="Unknown"
+-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	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/cgi-bin/interfaces/mopac.int.disabled	2005-12-03 14:57:07.000000000 -0800
+@@ -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	2005-11-21 07:40:28.000000000 -0800
++++ WebMO.install/cgi-bin/interfaces/tinker.int.disabled	2005-12-03 14:57:31.000000000 -0800
+@@ -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/metadata.xml b/sci-chemistry/webmo/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/webmo/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/webmo/webmo-6.0.003.ebuild b/sci-chemistry/webmo/webmo-6.0.003.ebuild
new file mode 100644
index 000000000000..22798675d2be
--- /dev/null
+++ b/sci-chemistry/webmo/webmo-6.0.003.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/webmo-6.0.003.ebuild,v 1.1 2005/12/04 08:27:33 spyderous 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}/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
+
+	# Comment out section of setup script that is interactive if run as root
+	epatch ${FILESDIR}/dont-be-interactive-if-root.patch
+
+	# Don't check for user directories, because we aren't installing in ~
+	epatch ${FILESDIR}/dont-check-unneeded-things.patch
+
+	# Make setup.conf
+	create_setup_conf
+}
+
+src_compile() {
+	# Doesn't compile, it's perl+html
+	true
+}
+
+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 ${MY_CGIBINDIR}/webmo/interfaces"
+	files=$(echo ${files} | sed -e "s:${D}::g")
+	for file in ${files}; do
+		webapp_configfile "${file}"
+		webapp_serverowned "${file}"
+	done
+
+	webapp_src_install
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Be sure that this line is uncommented in httpd.conf:"
+	einfo "AddHandle cgi-scripts .cgi"
+	einfo
+	einfo "The diagnose.pl script can be run if WebMO doesn't work properly."
+	einfo
+
+	webapp_pkg_postinst
+}
+
+create_setup_conf() {
+	local SETUP_CONF="${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}
+}