| 1 | |
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| 2 | Welcome to the ARB 6 Sequence Analysis Suite |
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| 3 | |
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| 4 | |
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| 5 | System Requirements |
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| 6 | ------------------- |
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| 7 | |
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| 8 | Minimal (demo.arb): |
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| 9 | Operating System: Linux or OSX |
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| 10 | CPU: any |
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| 11 | Memory: 1 GB |
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| 12 | Hard drive: 200 MB |
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| 13 | |
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| 14 | Recommended (SILVA SSU NR99 r115): |
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| 15 | Operating System: Linux (Ubuntu 12.04 or newer) |
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| 16 | OSX (10.5.8 or newer) |
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| 17 | CPU: >2 GHz multi-core |
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| 18 | Memory: 16 GB (or more!) |
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| 19 | Hard drive: 10 GB |
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| 20 | |
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| 21 | Notes: |
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| 22 | The resources required for ARB to run smoothly depend on the size of the |
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| 23 | database(s) you intend to work with. Large databases, especially the SSU |
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| 24 | databases provided by the SILVA project, require large amounts of fast |
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| 25 | memory. |
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| 26 | |
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| 27 | |
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| 28 | Installation using Package Managers: |
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| 29 | ---------------------------------- |
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| 30 | |
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| 31 | OSX: |
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| 32 | The recommended approach is to install MacPorts (macports.org) and use |
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| 33 | the ports command to install arb: "sudo port install arb" |
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| 34 | |
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| 35 | Debian Linux: |
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| 36 | ARB is available in Debian Testing in section "non-free". Install ARB |
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| 37 | using "apt-get install arb" or your preferred GUI front-end to apt-get. |
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| 38 | |
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| 39 | |
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| 40 | Installation from Pre-Compiled Binaries: |
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| 41 | ---------------------------------------- |
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| 42 | |
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| 43 | 1) Download "arb_install.sh" and the arb-*.tgz matching your distribution |
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| 44 | from http://download.arb-home.de/release/latest/ |
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| 45 | |
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| 46 | Files: |
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| 47 | arb-*.centos5-amd64.tgz |
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| 48 | arb-*.centos6-amd64.tgz |
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| 49 | arb-*.osx.tgz |
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| 50 | arb-*.ubuntu1004-amd64.tgz |
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| 51 | arb-*.ubuntu1204-amd64.tgz |
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| 52 | arb-*.ubuntu1304-amd64.tgz |
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| 53 | |
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| 54 | (where '*' stands for the most recent version number, e.g. '6.0.1') |
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| 55 | |
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| 56 | If your distribution is neither Ubuntu nor Centos, try Centos. |
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| 57 | If your distributions version is not among the above, try the next older |
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| 58 | release (e.g. 12.04 if you have 12.10). |
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| 59 | |
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| 60 | Notes: |
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| 61 | * All versions are compiled without OPENGL. |
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| 62 | (if you rely on OPENGL features, either stick with arb_5.5 or |
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| 63 | compile arb from source) |
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| 64 | * Debian users need to pick Centos (due to fun with [e]glibc) or better |
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| 65 | use the package from non-free. |
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| 66 | |
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| 67 | 2a) Install using "arb_install.sh" |
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| 68 | |
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| 69 | Open a terminal, change to the directory where you have saved the |
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| 70 | files needed for installation: |
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| 71 | |
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| 72 | 'arb_install.sh' // install script |
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| 73 | 'arb_README.txt' // this file |
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| 74 | 'arb-*.tgz' // your chosen ARB version |
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| 75 | |
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| 76 | and type |
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| 77 | |
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| 78 | sh arb_install.sh |
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| 79 | |
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| 80 | (to install arb for all users call the script as root or via sudo) |
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| 81 | |
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| 82 | Answer all questions asked by the script. |
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| 83 | |
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| 84 | Notes: |
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| 85 | - The script will ask about a pt_server directory. This is a |
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| 86 | directory where arb will store big index files. |
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| 87 | You should enter a different path as you do not want to |
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| 88 | recreate those files after an ARB update. |
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| 89 | - Normally pressing enter will be a good choice. |
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| 90 | - You can rerun the script many times, it can be used to |
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| 91 | change an existing installation. |
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| 92 | |
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| 93 | Change your ".cshrc" or ".profile" files: |
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| 94 | |
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| 95 | Set the environment variable ARBHOME to the ARB installation directory |
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| 96 | Append $ARBHOME/bin to your PATH. |
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| 97 | Re-Login to load the changed environment. |
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| 98 | |
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| 99 | Go to a directory with a demo database eg 'demo.arb'and start 'ARB' with |
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| 100 | |
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| 101 | arb |
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| 102 | |
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| 103 | 2b) Install manually |
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| 104 | |
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| 105 | i) Create a folder where you want ARB to reside. E.g: |
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| 106 | |
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| 107 | mkdir ~/arb-6.0 |
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| 108 | |
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| 109 | ii) Unpack ARB into this folder. E.g. |
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| 110 | |
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| 111 | tar -C ~/arb-6.0 -xzf ~/Downloads/arb-6.0.1.ubuntu1304-amd64.tgz |
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| 112 | |
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| 113 | iii) Install library dependencies. |
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| 114 | |
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| 115 | (If you already have an ARB installation and just want to install another |
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| 116 | version, you can skip this step.) |
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| 117 | |
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| 118 | ARB needs: |
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| 119 | gnuplot, gv, openmotif, xfig, transfig, xterm, libtiff, libX11, libXaw, |
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| 120 | libXext, libxml2, libXpm, libXt, lynx, time, libxslt, glib2, readline |
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| 121 | |
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| 122 | On Centos, dependencies should be satisfied by running: |
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| 123 | |
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| 124 | sudo yum install gnuplot openmotif xfig transfig xterm libXpm \ |
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| 125 | libtiff libX11 libXaw libXext libxml2 libXpml libXt lynx \ |
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| 126 | time libxslt readline glib2 |
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| 127 | |
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| 128 | On Ubuntu 13.04, use: |
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| 129 | |
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| 130 | sudo apt-get install gnuplot gv libmotif3 xfig transfig \ |
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| 131 | xterm libxpm4 libtiff4 libx11-6 libxaw7 libxext6 libxml2-utils \ |
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| 132 | libxt6 lynx libreadline6 |
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| 133 | |
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| 134 | If any of the packages is not available on your system, it might just |
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| 135 | have a slightly differing name. Try using "yum search" or |
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| 136 | "apt-cache search" to search for packages matching the base name |
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| 137 | (e.g. "yum search libxpm") and pick the one that's available. The only |
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| 138 | known issue is that you must not use "lesstif" instead of |
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| 139 | motif/openmotif (if you do, the interface will look broken). |
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| 140 | |
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| 141 | You can now run ARB simply by entering "./bin/arb" from the folder |
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| 142 | where you installed ARB. For convenience, put a symlink to the file |
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| 143 | into any folder that is in your PATH so that you can just type "arb" |
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| 144 | to run it. |
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| 145 | |
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| 146 | |
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| 147 | Compiling ARB from source |
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| 148 | ------------------------- |
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| 149 | |
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| 150 | * See arb_INSTALL.txt for information about how to compile |
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| 151 | arb from source. |
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| 152 | |
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| 153 | |
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| 154 | Additional information |
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| 155 | ---------------------- |
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| 156 | |
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| 157 | * See arb_INSTALL.txt for additional software needed and/or useful |
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| 158 | together with ARB. |
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| 159 | |
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| 160 | |
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| 161 | PT_server |
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| 162 | --------- |
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| 163 | |
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| 164 | To Install 'ARB' you have to know that some modules use a so |
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| 165 | called 'pt_server' (prefix tree server). |
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| 166 | |
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| 167 | ARB needs a writeable directory to store the pt_server files. |
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| 168 | Those files are needed for fast database search |
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| 169 | (by probe_design, probe_match and the automatic aligner) |
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| 170 | and need a lot of disc space (up to several 100 mega bytes, |
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| 171 | e.g. 4000 16S RNA sequences require about 40 MB). |
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| 172 | This files are not created now. They can be build by any user via |
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| 173 | <ARB_NTREE/Probes/PT_SERVER admin/Build server> |
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| 174 | You may define a special directory as the pt_server files location. |
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| 175 | This prevents any loss of data installing a new version of |
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| 176 | ARB. |
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| 177 | To minimize the use of resources in a workstation cluster |
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| 178 | only one pt_server for each database is started on a user defined |
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| 179 | host. The first user starts the pt_server, and all other users |
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| 180 | can connect to it. |
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| 181 | |
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| 182 | |
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| 183 | The Database |
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| 184 | ------------ |
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| 185 | |
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| 186 | In the current release a small dataset (demo.arb) is provided. |
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| 187 | This database contains a selection of artificial and real-life |
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| 188 | sequences. |
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| 189 | |
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| 190 | The intention of providing this small dataset first is to give |
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| 191 | you the opportunity to get familiar with the program and to |
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| 192 | test the performance of your computer system as well as the |
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| 193 | stability of ARB on your system. |
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| 194 | |
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| 195 | |
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| 196 | Bugs |
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| 197 | ---- |
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| 198 | |
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| 199 | ARB is running properly and stably on our systems. However, it |
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| 200 | may be that there are bugs never detected by us or never |
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| 201 | appearing on our systems. Please don't hesitate to inform us |
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| 202 | about any bugs. A detailed description of the steps performed |
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| 203 | before the problem was evident and of the number and types of |
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| 204 | modules running at the same time would be extremely helpful to |
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| 205 | our computer scientists. |
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| 206 | |
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| 207 | Please report bugs into our bug tracker at |
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| 208 | http://bugs.arb-home.de/ |
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| 209 | |
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| 210 | |
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| 211 | Support |
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| 212 | ------- |
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| 213 | |
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| 214 | Please send any comments, bug reports or questions to |
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| 215 | |
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| 216 | arb@arb-home.de |
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| 217 | |
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| 218 | |
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| 219 | Copyright Notice |
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| 220 | ---------------- |
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| 221 | |
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| 222 | Please see the file |
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| 223 | |
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| 224 | arb_LICENSE.txt |
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| 225 | |
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| 226 | in the ARB installation directory. |
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| 227 | |
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| 228 | |
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| 229 | Disclaimer |
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| 230 | ---------- |
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| 231 | |
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| 232 | THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED |
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| 233 | FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT |
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| 234 | NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF |
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| 235 | FITNESS FOR A PARTICULAR PURPOSE. |
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| 236 | |
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| 237 | |
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| 238 | Have fun! |
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| 239 | |
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| 240 | |
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