--- Portfile.orig 2009-10-09 23:30:39.000000000 -0400 +++ Portfile 2011-02-13 18:29:23.000000000 -0500 @@ -1,11 +1,11 @@ # -*- 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: Portfile 59128 2009-10-10 03:15:21Z macsforever2000@macports.org $ +# $Id$ PortSystem 1.0 name arb -version 5.1 epoch 1 +version 5.2 categories science maintainers me.com:matt.cottrell platforms darwin @@ -18,77 +18,98 @@ 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 \ + 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. -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 +master_sites http://download.arb-home.de/release/arb_${version}/ +distname arbsrc +extract.suffix .tgz +dist_subdir ${name}/${version} +worksrcdir arbsrc_6779 + +checksums sha1 4ee493a16ece5231d46ed1071407c06e733d67c8 \ + rmd160 d9d99d0ebadaa293091ff93f6ca588b2321bd8b0 + +depends_build port:gsed \ + port:imake \ + port:makedepend depends_lib port:openmotif \ port:lynx \ - port:gsed \ - port:imake \ port:sablotron \ port:mesa \ port:glw \ port:glew \ - port:tiff + port:tiff \ + port:xfig \ + port:gv patchfiles patch-ARB-config.makefile.diff \ patch-ARB-makefile.diff \ patch-ARB-RNA3D_GlobalHeader.hxx.diff \ - patch-ARB-DARWIN.pl.diff + patch-ARB-DARWIN.pl.diff \ + arb_intro.fig.diff \ + patch-ARB-glpng.diff + -worksrcdir stable_5.0 +platform darwin { + if {${build_arch} == "ppc" || ${build_arch} == "i386" } { + set is64bit 0 + if {${os.platform} == "darwin" && ${os.major} >= 9} { + if {[sysctl hw.cpu64bit_capable] == 1} { + ui_msg "64-bit capable hardware: Building 32-bit ARB. Check the setting of build_arch in ${prefix}/etc/macports/macports.conf" + } else { + ui_msg "not 64-bit capable hardware: Building 32-bit ARB." + } + } else { + ui_msg "unable to determine 64-bit hardware capability: Building 32-bit ARB." + } + } else { + set is64bit 1 + ui_msg "64-bit capable hardware: Building 64-bit ARB." + } +} + +configure { -use_configure no -configure.env ARBHOME=${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 + reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \ + ${worksrcpath}/util/arb_check_build_env.pl \ + ${worksrcpath}/arb_install.sh \ + ${worksrcpath}/WINDOW/AW_status.cxx \ + ${worksrcpath}/SH/example_batch_probe_match.sh \ + ${worksrcpath}/GDEHELP/GDEmenus \ + ${worksrcpath}/GDEHELP/genhelp.sh \ + ${worksrcpath}/GDEHELP/genhelptree.sh \ + ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh \ + ${worksrcpath}/HELP_SOURCE/Makefile \ + ${worksrcpath}/AISC_COM/AISC/Makefile \ + ${worksrcpath}/GDEHELP/Makefile \ + ${worksrcpath}/HELP_SOURCE/genhelp/Makefile \ + ${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 ${worksrcpath}/bin -} + reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL \ + ${worksrcpath}/bin/arb_macsetup -platform darwin 9 { -post-configure { - reinplace "s|ARB_64 := 1# compile 64bit ARB version|ARB_64 := 0# compile 64bit ARB version|g" ${worksrcpath}/config.makefile -} + reinplace "s|OSX_SDK:=/Developer/SDKs/MacOSX10.5.sdk|OSX_SDK:=${configure.sdkroot}|g" ${worksrcpath}/Makefile + + reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile } -build.env-append ${configure.env} -build.env-append PREFIX=${prefix} +build.env-append PREFIX=${prefix} \ + ARBHOME=${worksrcpath} \ + PATH=${worksrcpath}/bin:$env(PATH) + +build.args GCC=${configure.cc} \ + GPP=${configure.cxx} \ + CPPreal=${configure.cpp} 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 @@ -97,33 +118,30 @@ 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" + 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 + system "rm -rf `find ${destroot}${prefix}/share/arb -type d -name .svn`" } - -post-activate { - system "rm -rf `find ${prefix}/share/arb -type d -name .svn`" -ui_msg " +universal_variant no + +notes " **************************************************************** Before running ARB you must set ARBHOME and add ARB to your PATH **************************************************************** You have two options (A is easier, B is more difficult): -A) Open a new terminal window and type arb_macsetup to set up your environment automatically +A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically. This script also enables keyboard shortcuts used in the sequence editor. or -B) Follow the steps below: +B) More difficult - follow the steps below: -1a) +1) bash users add the following lines to your ~/.profile or to your ~/.bashrc ARBHOME=${prefix}/share/arb;export ARBHOME @@ -132,18 +150,31 @@ enter the following command: . ~/.profile -1b) +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 -2) +3) +create 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 + +C) +to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup + +D) 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 " -} \ No newline at end of file