View the most recent changes for the arb port at: arb.darwinports.com/diff
Scroll down toward the bottom of the page to get installation instructions for arb.
The raw portfile for arb 5.1 is located here:
http://arb.darwinports.com/dports/science/arb/Portfile
Find related portfiles with the unique DarwinPorts.com search feature.
Check for any related Fink projects here: pdb.finkproject.org/pdb/package.php/arb

# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
The arb Portfile 59128 2009-10-10 03:15:21Z macsforever2000 macports.org $

PortSystem 1.0

Name: arb
Version: 5.1
epoch 1
Category: science
Maintainers: me.com:matt.cottrell
Platform: darwin

Description: ARB graphical DNA, RNA and amino acid sequence analysis tool

Homepage: http://www.arb-home.de/

Long Description: ARB is an application for genetic sequence analysis that includes tools for editing and aligning nucleotide and amino acid sequences. Features include routines for designing fluorescence in situ hybridization (FISH) probes and PCR and sequencing primers. Phylogenetic trees can be generated and sequences can be added to existing trees. ARB maintains links between the phylogenetic trees and sequences for data base search and query. The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) maintaines up-to-date databases. 64-bit ARB is built on 10.6 in order to work with the largest data bases. 32-bit ARB is built on 10.5. An active community of scientists exchange tips on the ARB Yahoo! discussion group (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371.

fetch.type svn
svn.url http://svn.mikro.biologie.tu-muenchen.de/svn/branches/stable_5.0
svn.revision 6215
svn.method checkout
#fetch.user coder
#fetch.password gimmeARBsource
#work around until ticket #21232 is resolved
svn.args --username coder --password gimmeARBsource

depends_lib port:openmotif port:lynx port:gsed port:imake port:sablotron port:mesa port:glw port:glew port:tiff

Patch Files: patch-ARB-config.makefile.diff patch-ARB-makefile.diff patch-ARB-RNA3D_GlobalHeader.hxx.diff patch-ARB-DARWIN.pl.diff

worksrcdir stable_5.0

use_configure no
configure.env ARBHOME=${worksrcpath}
configure.env-append PATH=${worksrcpath}/bin:$env(PATH)

configure {
reinplace "s| PREFIX |${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu
reinplace "s| sed | gsed |g" ${worksrcpath}/util/arb_check_build_env.pl
reinplace "s| sed | gsed |g" ${worksrcpath}/arb_install.sh
reinplace "s| sed | gsed |g" ${worksrcpath}/WINDOW/AW_status.cxx
reinplace "s| sed | gsed |g" ${worksrcpath}/SH/example_batch_probe_match.sh
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/GDEmenus
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelp.sh
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelptree.sh
reinplace "s| sed | gsed |g" ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh
reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/Makefile
reinplace "s| sed | gsed |g" ${worksrcpath}/AISC_COM/AISC/Makefile
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile
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 {
post-configure {
reinplace "s|ARB_64 := 1# compile 64bit ARB version|ARB_64 := 0# compile 64bit ARB version|g" ${worksrcpath}/config.makefile
}
}

build.env-append ${configure.env}
build.env-append PREFIX=${prefix}

destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts

destroot {
eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin
file mkdir ${destroot}${prefix}/share/arb
file mkdir ${destroot}${prefix}/share/arb/bin
file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib
file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
file mkdir ${destroot}${prefix}/lib/help
file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help
file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS
file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH
file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb
}

post-destroot {
system "chmod a+w ${destroot}${prefix}/share/arb/lib/arb_tcp.dat"
system "chmod a+w ${destroot}${prefix}/share/arb/lib/pts"
system "chmod a+w ${destroot}${prefix}/share/arb/lib/macros"
system "ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server"
system "ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server"
}

post-activate {
system "rm -rf `find ${prefix}/share/arb -type d -name .svn`"

ui_msg "
****************************************************************
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
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
2)
type arb to start ARB

A demo data base is located at ${prefix}/share/arb.demo.arb

Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
"
}

If you haven't already installed Darwin Ports, you can find easy instructions for doing so at the main Darwin Ports page.
Once Darwin Ports has been installed, in a terminal window and while online, type the following and hit return:

%  cd /opt/local/bin/portslocation/dports/arb
%  sudo port install arb  
Password: 

You will then be prompted for your root password, which you should enter. You may have to wait for a few minutes while the software is retrieved from the network and installed for you. Y ou should see something that looks similar to:

--->  Fetching arb
--->  Verifying checksum for arb
--->  Extracting arb
--->  Configuring arb
--->  Building arb with target all

--->  Staging arb into destroot

--->  Installing arb

- Make sure that you do not close the terminal window while Darwin Ports is working. Once the software has been installed, you can find further information about using arb with these commands:

%  man arb
%  apropos arb
%  which arb
%  locate arb

 Where to find more information: