[59128] trunk/dports/science/arb
macsforever2000 at macports.org
macsforever2000 at macports.org
Fri Oct 9 20:15:23 PDT 2009
Revision: 59128
http://trac.macports.org/changeset/59128
Author: macsforever2000 at macports.org
Date: 2009-10-09 20:15:21 -0700 (Fri, 09 Oct 2009)
Log Message:
-----------
Maintainer update to version 5.1. (#21807)
Modified Paths:
--------------
trunk/dports/science/arb/Portfile
Added Paths:
-----------
trunk/dports/science/arb/files/arb_macsetup
Modified: trunk/dports/science/arb/Portfile
===================================================================
--- trunk/dports/science/arb/Portfile 2009-10-10 03:12:32 UTC (rev 59127)
+++ trunk/dports/science/arb/Portfile 2009-10-10 03:15:21 UTC (rev 59128)
@@ -4,7 +4,8 @@
PortSystem 1.0
name arb
-version 5.19.0
+version 5.1
+epoch 1
categories science
maintainers me.com:matt.cottrell
platforms darwin
@@ -25,7 +26,7 @@
fetch.type svn
svn.url http://svn.mikro.biologie.tu-muenchen.de/svn/branches/stable_5.0
-svn.revision 6192
+svn.revision 6215
svn.method checkout
#fetch.user coder
#fetch.password gimmeARBsource
@@ -70,6 +71,8 @@
reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/genhelp/Makefile
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile.helpfiles
file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
+ reinplace "s|@@PREFIX@@|${prefix}|g" ${filespath}/arb_macsetup
+ file copy ${filespath}/arb_macsetup ${worksrcpath}/bin
}
platform darwin 9 {
@@ -106,30 +109,38 @@
post-activate {
system "rm -rf `find ${prefix}/share/arb -type d -name .svn`"
+
ui_msg "
-1)
-**************************************************************************
-bash-users add the following lines to your ~/.profile or to your ~/.bashrc
-**************************************************************************
+****************************************************************
+Before running ARB you must set ARBHOME and add ARB to your PATH
+****************************************************************
+
+You have two options (A is easier, B is more difficult):
+
+A) Open a new terminal window and type arb_macsetup to set up your environment automatically
+
+or
+
+B) Follow the steps below:
+
+1a)
+bash users add the following lines to your ~/.profile or to your ~/.bashrc
+
ARBHOME=${prefix}/share/arb;export ARBHOME
PATH=${prefix}/share/arb/bin:\$PATH
export PATH
enter the following command:
. ~/.profile
-2)
-**************************************************
+1b)
tcsh users add the following lines to your ~/.cshrc
-**************************************************
setenv ARBHOME ${prefix}/share/arb
setenv PATH ${prefix}/share/arb\:\$PATH
enter the following command:
source ~/.cshrc
-3)
-*********************
+2)
type arb to start ARB
-*********************
A demo data base is located at ${prefix}/share/arb.demo.arb
Added: trunk/dports/science/arb/files/arb_macsetup
===================================================================
--- trunk/dports/science/arb/files/arb_macsetup (rev 0)
+++ trunk/dports/science/arb/files/arb_macsetup 2009-10-10 03:15:21 UTC (rev 59128)
@@ -0,0 +1,165 @@
+#!/bin/bash
+#
+# Copyright (c) 2002-2007 Juan Manuel Palacios <jmpp at macports.org>, The MacPorts Project.
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# 3. Neither the name of Apple, Inc., The MacPorts Project nor the
+# names of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+# OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+# SUCH DAMAGE.
+#
+
+# This is the arb_macsetup script
+# Use it to set the ARBHOME and PATH variables after installing ARB using MacPorts.
+
+# Derived from the MacPorts postflight script
+# Provided by: Matthew Cottrell
+# October 1, 2009
+
+# Abstraction variables:
+# The MacPorts PREFIX is typicaly /opt/local
+PREFIX=/opt/local
+BINPATH=${PREFIX}/bin
+SBINPATH=${PREFIX}/sbin
+MANPAGES=${PREFIX}/share/man
+TIMESTAMP=$(date +"%Y-%m-%d_at_%H:%M:%S")
+BACKUP_SUFFIX=macports-saved_${TIMESTAMP}
+OUR_STRING="ARB Installer addition on ${TIMESTAMP}"
+
+# Determine the user's shell, in order to choose an appropriate configuration file we'll be tweaking.
+# Exit nicely if the shell is any other than bash or tcsh, as that's considered non-standard.
+USHELL=$(dscl . -read /users/${USER} shell | awk -F'/' '{print $NF}') || {
+ echo "An attempt to determine your shell name failed! Please set your ARB compatible environment manually."
+ exit 1
+}
+case "${USHELL}" in
+ tcsh)
+ echo "Detected the tcsh shell."
+ LOGIN_FLAG=""
+ ENV_COMMAND="setenv"
+ ASSIGN=" "
+ if [ -f ${HOME}/.tcshrc ]; then
+ CONF_FILE=tcshrc
+ elif [ -f ${HOME}/.cshrc ]; then
+ CONF_FILE=cshrc
+ else
+ CONF_FILE=tcshrc
+ fi
+ ;;
+ bash)
+ echo "Detected the bash shell."
+ LOGIN_FLAG="-l"
+ ENV_COMMAND="export"
+ ASSIGN="="
+ if [ -f ${HOME}/.bash_profile ]; then
+ CONF_FILE=bash_profile
+ elif [ -f ${HOME}/.bash_login ]; then
+ CONF_FILE=bash_login
+ else
+ CONF_FILE=profile
+ fi
+ ;;
+ *)
+ echo "Unknown shell ($USHELL)! Please set your ARB compatible environment manually."
+
+ exit 0
+ ;;
+esac
+
+# Through this command we write an environment variable to an appropriate shell configuration file,
+# backing up the original only if it exists and if it doesn't contain the ${OUR_STRING} identification string,
+# which hints that we've already tweaked it and therefore already backed it up.
+function write_setting () {
+ if [ -f ${HOME}/.${CONF_FILE} ] && ! grep "${OUR_STRING}" ${HOME}/.${CONF_FILE} > /dev/null; then
+ echo "Backing up your ${HOME}/.${CONF_FILE} shell confguration file as ${HOME}/.${CONF_FILE}.${BACKUP_SUFFIX} before adapting it for ARB."
+ /bin/cp -fp ${HOME}/.${CONF_FILE} "${HOME}/.${CONF_FILE}.${BACKUP_SUFFIX}" || {
+ echo "An attempt to backup your original configuration file failed! Please set your ARB compatible environment manually."
+
+ exit 1
+ }
+ echo -e "\n##\n# Your previous ${HOME}/.${CONF_FILE} file was backed up as ${HOME}/.${CONF_FILE}.${BACKUP_SUFFIX}\n##" >> ${HOME}/.${CONF_FILE}
+ fi
+ echo -e "\n# ${OUR_STRING}: adding an appropriate ${1} variable for use with ${3}." >> ${HOME}/.${CONF_FILE}
+ echo "${ENV_COMMAND} ${1}${ASSIGN}${2}" >> ${HOME}/.${CONF_FILE}
+ echo -e "# Finished adapting your ${1} environment variable for use with ARB.\n" >> ${HOME}/.${CONF_FILE}
+ chown ${USER} ${HOME}/.${CONF_FILE} || echo "Warning: unable to adapt permissions on your ${HOME}/.${CONF_FILE} shell configuration file!"
+ echo "An appropriate ${1} variable has been added to your shell environment by the ${3} installer."
+}
+
+# Confirm that MacPorts has been configured for this user:
+if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv PATH" | grep ${PREFIX} > /dev/null; then
+ echo "Your shell already has the right PATH environment variable for use with MacPorts!"
+else
+ echo "Uh oh! MacPorts is not configured for this user"
+ echo "Setting up MacPorts and ARB"
+ # Adding our setting to the PATH variable if not already there:
+ write_setting PATH "${BINPATH}:${SBINPATH}:\$PATH" MacPorts
+
+ # We gather the path into a variable of our own for faster operation:
+ ORIGINAL_MANPATH="$(${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv MANPATH")"
+ # Adding our setting to the MANPATH variable only if it exists:
+ if ! ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/env | grep MANPATH" > /dev/null || \
+ # and following that, if it's not empty:
+ [ -z "${ORIGINAL_MANPATH}" ] || \
+ # or if it doesn't already contain our path:
+ echo "${ORIGINAL_MANPATH}" | grep ${MANPAGES} > /dev/null || \
+ # or if there's no empty component somewhere in the middle of it:
+ echo "${ORIGINAL_MANPATH}" | grep :: > /dev/null || \
+ # or at the start of it:
+ [ -z "$(echo "${ORIGINAL_MANPATH}" | awk -F : '{print $1}')" ] || \
+ # or at the end of it:
+ [ -z "$(echo "${ORIGINAL_MANPATH}" | awk -F : '{print $NF}')" ]; then
+ echo "Your shell already has the right MANPATH environment variable for use with MacPorts!"
+ else
+ write_setting MANPATH "${MANPAGES}:\$MANPATH"
+ fi
+ echo "Done setting up MacPorts"
+fi
+
+# Adding ARB path to the PATH variable if it is not already there:
+if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv PATH" | grep ${PREFIX}/share/arb/bin > /dev/null; then
+ echo "Your shell already has the right PATH environment variable for use with ARB!"
+else
+ write_setting PATH "${PREFIX}/share/arb/bin:\$PATH" ARB
+fi
+
+# Adding the ARBHOME variable if not already there:
+if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv ARBHOME" | grep ${PREFIX}/share/arb > /dev/null; then
+ echo "Your shell already has the right ARBHOME environment variable for use with ARB!"
+else
+ write_setting ARBHOME "${PREFIX}/share/arb" ARB
+fi
+
+# arb_setenv script is done with its job - exit gracefully!
+echo ""
+echo "You have succesfully installed ARB"
+echo ""
+echo "Open a new terminal window and type arb to launch ARB"
+echo ""
+echo "A demo data base is located at ${prefix}/share/arb.demo.arb"
+echo ""
+echo "************************************************************************************************"
+echo "Note: To set up ARB for another user log into their account and type ${prefix}/bin/arb_macsetup"
+echo "************************************************************************************************"
+echo ""
+echo "Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371"
+exit 0
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