| 1 | # -*- 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 |
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| 2 | # $Id$ |
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| 3 | |
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| 4 | PortSystem 1.0 |
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| 5 | |
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| 6 | name arb |
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| 7 | epoch 1 |
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| 8 | version 5.2 |
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| 9 | revision 2 |
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| 10 | categories science |
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| 11 | maintainers me.com:matt.cottrell |
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| 12 | platforms darwin |
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| 13 | |
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| 14 | description ARB graphical DNA, RNA and amino acid sequence analysis tool |
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| 15 | |
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| 16 | homepage http://www.arb-home.de/ |
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| 17 | |
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| 18 | long_description ARB is an application for genetic sequence analysis that includes tools for editing and aligning \ |
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| 19 | nucleotide and amino acid sequences. Features include routines for designing fluorescence in situ \ |
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| 20 | hybridization (FISH) probes and PCR and sequencing primers. Phylogenetic trees can be generated and \ |
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| 21 | sequences can be added to existing trees. ARB maintains links between the phylogenetic trees and sequences \ |
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| 22 | for database search and query. The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \ |
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| 23 | maintains up-to-date databases. An active community of scientists exchanges tips on the ARB Yahoo! discussion group \ |
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| 24 | (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \ |
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| 25 | for sequence data. Nucleic Acids Research. 32:1363-1371. |
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| 26 | |
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| 27 | master_sites http://download.arb-home.de/release/arb_${version}/ |
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| 28 | distname arbsrc |
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| 29 | extract.suffix .tgz |
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| 30 | dist_subdir ${name}/${version} |
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| 31 | worksrcdir arbsrc_6779 |
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| 32 | |
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| 33 | checksums sha1 4ee493a16ece5231d46ed1071407c06e733d67c8 \ |
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| 34 | rmd160 d9d99d0ebadaa293091ff93f6ca588b2321bd8b0 |
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| 35 | |
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| 36 | depends_build port:imake \ |
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| 37 | port:makedepend |
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| 38 | |
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| 39 | depends_lib port:openmotif \ |
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| 40 | port:lynx \ |
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| 41 | port:gsed \ |
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| 42 | port:sablotron \ |
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| 43 | port:mesa \ |
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| 44 | port:glw \ |
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| 45 | port:glew \ |
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| 46 | port:tiff \ |
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| 47 | port:libpng \ |
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| 48 | port:xfig \ |
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| 49 | port:gv \ |
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| 50 | port:xorg-libXaw |
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| 51 | |
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| 52 | patchfiles patch-ARB-config.makefile.diff \ |
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| 53 | patch-ARB-makefile.diff \ |
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| 54 | patch-ARB-RNA3D_GlobalHeader.hxx.diff \ |
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| 55 | patch-ARB-DARWIN.pl.diff \ |
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| 56 | patch-ARB-glpng.diff \ |
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| 57 | arb_intro.fig.diff \ |
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| 58 | patch-ARB-Flatio.diff \ |
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| 59 | patch-ARB-Zuk_to_gen.c.diff \ |
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| 60 | patch-ARB-count.c.diff \ |
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| 61 | patch-ARB-lsadt.c.diff \ |
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| 62 | patch-ARB-interface.c.diff |
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| 63 | |
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| 64 | configure { |
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| 65 | reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \ |
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| 66 | ${worksrcpath}/util/arb_check_build_env.pl \ |
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| 67 | ${worksrcpath}/arb_install.sh \ |
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| 68 | ${worksrcpath}/WINDOW/AW_status.cxx \ |
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| 69 | ${worksrcpath}/SH/example_batch_probe_match.sh \ |
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| 70 | ${worksrcpath}/GDEHELP/GDEmenus \ |
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| 71 | ${worksrcpath}/GDEHELP/genhelp.sh \ |
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| 72 | ${worksrcpath}/GDEHELP/genhelptree.sh \ |
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| 73 | ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh \ |
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| 74 | ${worksrcpath}/HELP_SOURCE/Makefile \ |
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| 75 | ${worksrcpath}/AISC_COM/AISC/Makefile \ |
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| 76 | ${worksrcpath}/GDEHELP/Makefile \ |
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| 77 | ${worksrcpath}/HELP_SOURCE/genhelp/Makefile \ |
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| 78 | ${worksrcpath}/GDEHELP/Makefile.helpfiles |
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| 79 | file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile |
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| 80 | file copy ${filespath}/arb_macsetup ${worksrcpath}/bin |
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| 81 | reinplace "s|@@LIBPERLDIR@@|[exec ${prefix}/bin/perl -e "use Config; print \$Config{archlib};"]/CORE|g" ${worksrcpath}/PERL2ARB/DARWIN.PL |
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| 82 | reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/bin/arb_macsetup |
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| 83 | |
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| 84 | reinplace "s|OSX_SDK:=/Developer/SDKs/MacOSX10.5.sdk|OSX_SDK:=${configure.sdkroot}|g" ${worksrcpath}/Makefile |
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| 85 | |
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| 86 | if {${build_arch} == "ppc" || ${build_arch} == "i386"} { |
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| 87 | set is64bit 0 |
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| 88 | } else { |
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| 89 | set is64bit 1 |
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| 90 | } |
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| 91 | reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile |
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| 92 | } |
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| 93 | |
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| 94 | build.env-append PREFIX=${prefix} \ |
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| 95 | ARBHOME=${worksrcpath} \ |
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| 96 | PATH=${worksrcpath}/bin:$env(PATH) |
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| 97 | |
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| 98 | if {${configure.compiler} == "clang" || |
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| 99 | ${configure.compiler} == "llvm-gcc-4.2"} { |
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| 100 | configure.compiler clang |
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| 101 | if {![file executable ${configure.cc}]} { |
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| 102 | depends_build-append port:apple-gcc42 |
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| 103 | configure.compiler apple-gcc-4.2 |
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| 104 | } |
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| 105 | } |
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| 106 | |
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| 107 | build.args GCC=${configure.cc} \ |
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| 108 | GPP=${configure.cxx} \ |
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| 109 | CPPreal=${configure.cpp} |
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| 110 | |
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| 111 | destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts |
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| 112 | destroot { |
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| 113 | # Give the default settings a recognizable name ending in .default |
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| 114 | file rename ${worksrcpath}/lib/arb_tcp.dat ${worksrcpath}/lib/arb_tcp.dat.default |
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| 115 | file rename ${worksrcpath}/lib/macros ${worksrcpath}/lib/macros.default |
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| 116 | |
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| 117 | eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin |
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| 118 | file mkdir ${destroot}${prefix}/share/arb/bin |
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| 119 | file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib |
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| 120 | file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP |
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| 121 | file mkdir ${destroot}${prefix}/lib/help |
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| 122 | file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help |
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| 123 | file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS |
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| 124 | file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH |
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| 125 | file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb |
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| 126 | ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server |
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| 127 | ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server |
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| 128 | xinstall -m 777 -d ${destroot}${prefix}/share/arb/lib/pts |
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| 129 | } |
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| 130 | |
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| 131 | # to be investigated later |
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| 132 | universal_variant no |
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| 133 | |
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| 134 | post-activate { |
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| 135 | # Provide users with copies of the default configuration and macros |
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| 136 | # if the user doesn't already have them. |
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| 137 | if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} { |
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| 138 | xinstall -m 777 ${prefix}/share/arb/lib/arb_tcp.dat.default \ |
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| 139 | ${prefix}/share/arb/lib/arb_tcp.dat |
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| 140 | } |
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| 141 | if {![file exists ${prefix}/share/arb/lib/macros]} { |
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| 142 | file copy ${prefix}/share/arb/lib/macros.default \ |
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| 143 | ${prefix}/share/arb/lib/macros |
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| 144 | fs-traverse item ${prefix}/share/arb/lib/macros { |
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| 145 | file attributes ${item} -permissions a+w |
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| 146 | } |
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| 147 | } |
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| 148 | } |
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| 149 | |
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| 150 | notes " |
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| 151 | **************************************************************** |
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| 152 | Before running ARB you must set ARBHOME and add ARB to your PATH |
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| 153 | **************************************************************** |
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| 154 | |
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| 155 | You have two options (A is easier, B is more difficult): |
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| 156 | |
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| 157 | A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically. This script also enables keyboard shortcuts used in the sequence editor. |
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| 158 | |
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| 159 | or |
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| 160 | |
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| 161 | B) More difficult - follow the steps below: |
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| 162 | |
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| 163 | 1) |
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| 164 | bash users add the following lines to your ~/.profile or to your ~/.bashrc |
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| 165 | |
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| 166 | ARBHOME=${prefix}/share/arb;export ARBHOME |
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| 167 | PATH=${prefix}/share/arb/bin:\$PATH |
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| 168 | export PATH |
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| 169 | |
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| 170 | enter the following command: |
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| 171 | . ~/.profile |
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| 172 | 2) |
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| 173 | tcsh users add the following lines to your ~/.cshrc |
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| 174 | |
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| 175 | setenv ARBHOME ${prefix}/share/arb |
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| 176 | setenv PATH ${prefix}/share/arb\:\$PATH |
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| 177 | |
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| 178 | enter the following command: |
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| 179 | source ~/.cshrc |
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| 180 | 3) |
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| 181 | create a text file in your home folder called .xmodmap that contains the text below: |
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| 182 | |
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| 183 | clear Mod1 |
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| 184 | clear Mod2 |
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| 185 | keycode 63 = Mode_switch |
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| 186 | keycode 66 = Meta_L |
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| 187 | keycode 69 = Meta_R |
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| 188 | add Mod1 = Meta_L Meta_R |
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| 189 | add Mod2 = Mode_switch |
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| 190 | |
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| 191 | C) |
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| 192 | to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup |
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| 193 | |
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| 194 | D) |
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| 195 | type arb to start ARB |
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| 196 | |
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| 197 | A demo data base is located at ${prefix}/share/arb/demo.arb |
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| 198 | |
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| 199 | ************************************************************************ |
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| 200 | User generated macros, arb_tcp.dat and pt_servers have been preserved, |
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| 201 | but you should keep backups of these just in case. They are located at: |
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| 202 | |
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| 203 | ${prefix}/share/arb/lib/macros/ |
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| 204 | ${prefix}/share/arb/lib/arb_tcp.dat |
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| 205 | ${prefix}/share/arb/lib/pts/ |
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| 206 | |
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| 207 | Default settings are maintained at: |
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| 208 | |
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| 209 | ${prefix}/share/arb/lib/macros.default/ |
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| 210 | ${prefix}/share/arb/lib/arb_tcp.dat.default |
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| 211 | |
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| 212 | Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371 |
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| 213 | " |
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| 214 | |
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| 215 | livecheck.type regex |
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| 216 | livecheck.url http://download.arb-home.de/release/ |
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| 217 | livecheck.regex ${name}_(\[0-9.\]+)/ |
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