# -*- 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 # $Id$ PortSystem 1.0 PortGroup compiler_blacklist_versions 1.0 name arb epoch 2 version 6.0.4 categories science maintainers mac.com:matt.cottrell platforms 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 database search and query. The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \ maintains up-to-date databases. An active community of scientists exchanges 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. license Restrictive/Distributable master_sites http://download.arb-home.de/release/${name}-${version}/ distname arb-${version}-source extract.suffix .tgz worksrcdir arbsrc_14797 checksums rmd160 a7e6ba2dff3eceba97d17e076c3efb333930dd72 \ sha256 875301f138974694144b11091b0303a22efcfe7c6291c438881da64179820ce0 # bin/mix conflicts elixir depends_build port:makedepend \ port:pkgconfig depends_lib port:openmotif \ port:lynx \ port:gsed \ port:sablotron \ port:glw \ port:glew \ port:xfig \ port:gv \ port:xorg-libXaw \ port:gtime \ path:lib/pkgconfig/glib-2.0.pc:glib2 \ port:coreutils patchfiles patch-ARB-config.makefile.diff \ patch-ARB-intro.fig.diff \ patch-ARB-arb.diff platform darwin { if {${os.major} < 11} { depends_build-append port:coreutils configure.env-append INSTALL=${prefix}/bin/ginstall } } # https://trac.macports.org/ticket/44368 platform darwin 11 { pre-patch { # DOS to UNIX line endings so we can patch. reinplace "s|\r||g" ${worksrcpath}/GDE/MUSCLE/src/globalsosx.cpp } patchfiles-append patch-ARB-globalsosx.cpp.diff } configure { if {${build_arch} eq "ppc" || ${build_arch} eq "i386"} { set is64bit 0 } else { set is64bit 1 } file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/SH/arb_macsetup } build.env-append PREFIX=${prefix} \ ARBHOME=${worksrcpath} \ PATH=${worksrcpath}/bin:$env(PATH) compiler.blacklist *gcc-4.0 *gcc-4.2 {clang < 138} build.args-append CXX=${configure.cxx} \ CC=${configure.cc} destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts destroot { # Give the default settings a recognizable name ending in .default file rename ${worksrcpath}/lib/arb_tcp.dat ${worksrcpath}/lib/arb_tcp.dat.default file rename ${worksrcpath}/lib/macros ${worksrcpath}/lib/macros.default xinstall -m 0755 {*}[glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin file mkdir ${destroot}${prefix}/share/arb/bin file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb file mkdir ${destroot}${prefix}/lib/help file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server ln -s ${prefix}/bin/muscle ${destroot}${prefix}/share/arb/bin/muscle xinstall -m 777 -d ${destroot}${prefix}/share/arb/lib/pts } # to be investigated later universal_variant no post-activate { # Provide users with copies of the default configuration and macros # if the user doesn't already have them. if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} { xinstall -m 777 ${prefix}/share/arb/lib/arb_tcp.dat.default \ ${prefix}/share/arb/lib/arb_tcp.dat } if {![file exists ${prefix}/share/arb/lib/macros]} { file copy ${prefix}/share/arb/lib/macros.default \ ${prefix}/share/arb/lib/macros fs-traverse item ${prefix}/share/arb/lib/macros { file attributes ${item} -permissions a+w } } } notes " **************************************************************** Before running ARB you must set ARBHOME and add ARB to your PATH **************************************************************** You have two options (A is easier, B is more difficult): A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically. This script also enables keyboard shortcuts used in the sequence editor. or B) More difficult - follow the steps below: 1) bash users add the following lines to your ~/.profile or to your ~/.bashrc ARBHOME=${prefix}/share/arb;export ARBHOME PATH=${prefix}/share/arb/bin:\$PATH export PATH enter the following command: . ~/.profile 2) 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 C) to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup ************************************************************************************************************************************ You can set up keyboard shortcuts manually by creating a text file in your home folder called .xmodmap that contains the text below: ************************************************************************************************************************************ clear Mod1 clear Mod2 keycode 63 = Mode_switch keycode 66 = Meta_L keycode 69 = Meta_R add Mod1 = Meta_L Meta_R add Mod2 = Mode_switch ******************************************************************* Use keys Control+Command Arrow Key to jump over bases Use Keys Option Arrow Key to pull in bases across alignment gaps Use the right Command Key plus a letter key to activate a menu item ******************************************************************* ***************************** Type 'arb' to start using ARB ***************************** A demo data base is located at ${prefix}/share/arb/demo.arb User generated macros, arb_tcp.dat and pt_servers have been preserved, but you should keep backups of these just in case. They are located at: ${prefix}/share/arb/lib/macros/ ${prefix}/share/arb/lib/arb_tcp.dat ${prefix}/share/arb/lib/pts/ Default settings are maintained at: ${prefix}/share/arb/lib/macros.default/ ${prefix}/share/arb/lib/arb_tcp.dat.default These notes can be viewed at any time by typing 'port notes arb' Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371 " livecheck.type regex livecheck.url http://download.arb-home.de/build/ livecheck.regex ${name}-(\[0-9.\]+)