| 1 | |
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| 2 | Welcome to the 'ARB' Sequence Database Tools |
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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 | |
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| 9 | ARB is currently developed for Linux and OSX. |
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| 10 | |
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| 11 | Hardware Requirements (Linux): |
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| 12 | |
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| 13 | Good We use |
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| 14 | Real memory : 1 Gb 4 Gb |
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| 15 | Free discspace : 1 Gb more |
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| 16 | Computer speed : 2 GHz Cpu 2 GHz Dual Cpu |
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| 17 | |
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| 18 | |
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| 19 | Note : Memory is more important than a fast processor! |
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| 20 | |
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| 21 | |
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| 22 | Files needed to install ARB |
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| 23 | --------------------------- |
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| 24 | |
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| 25 | File |
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| 26 | |
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| 27 | 'arb_install.sh' // install script |
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| 28 | 'arb-*.tgz' // ARB program |
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| 29 | |
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| 30 | |
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| 31 | Available ARB versions: |
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| 32 | |
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| 33 | arb-*.centos5-amd64.tgz |
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| 34 | arb-*.centos6-amd64.tgz |
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| 35 | arb-*.ubuntu1004-amd64.tgz |
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| 36 | arb-*.ubuntu1204-amd64.tgz |
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| 37 | arb-*.ubuntu1304-amd64.tgz |
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| 38 | arb-*.osx.tgz |
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| 39 | |
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| 40 | You need exactly ONE of the available 'arb-*.tgz'! |
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| 41 | |
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| 42 | Notes: |
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| 43 | |
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| 44 | * all versions are 64bit versions |
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| 45 | (if you really need a 32bit version, see http://download.arb-home.de/release/arb_5.5/) |
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| 46 | |
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| 47 | * all versions are compile without OPENGL |
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| 48 | (if you rely on OPENGL features, either stick with arb_5.5 or compile arb from source) |
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| 49 | |
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| 50 | * OSX version is available as arb-*.osx.tgz |
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| 51 | and via MacPorts (see arb_OS_X_MacPorts.txt included inside arb-*.osx.tgz) |
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| 52 | |
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| 53 | |
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| 54 | Install/Update ARB |
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| 55 | ------------------ |
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| 56 | |
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| 57 | ARB consists of more than 1400 files which are installed into a single |
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| 58 | directory. Creating this directory, copying all data into it, and setting |
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| 59 | the permissions correctly is done by the installation script |
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| 60 | |
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| 61 | 'arb_install.sh' |
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| 62 | |
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| 63 | Open a terminal, change to the directory where you have saved the |
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| 64 | files needed for installation: |
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| 65 | |
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| 66 | 'arb_install.sh' // install script |
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| 67 | 'arb_README.txt' // this file |
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| 68 | 'arb-*.tgz' // your chosen ARB version |
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| 69 | |
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| 70 | |
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| 71 | and type |
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| 72 | |
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| 73 | '/bin/sh arb_install.sh' |
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| 74 | |
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| 75 | (to install arb for all users call the script as root or via sudo) |
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| 76 | |
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| 77 | |
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| 78 | Answer all questions asked by the script. |
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| 79 | |
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| 80 | Notes:- The script will ask about a pt_server directory. This is a |
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| 81 | directory where arb will store big index files. |
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| 82 | You should enter a different path as you do not want to |
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| 83 | recreate those files after an ARB update. |
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| 84 | - Normally pressing enter will be a good choice. |
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| 85 | - You can rerun the script many times, it can be used to |
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| 86 | change an existing installation. |
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| 87 | |
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| 88 | Change your .cshrc/.profile files: |
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| 89 | |
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| 90 | Set the environment variable ARBHOME |
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| 91 | to the ARB installation directory |
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| 92 | Append $ARBHOME/bin to your PATH |
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| 93 | |
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| 94 | reread it, (logout+login) |
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| 95 | |
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| 96 | goto a directory with a demo database 'eg demo.arb' |
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| 97 | and start 'ARB' with |
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| 98 | |
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| 99 | 'arb' |
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| 100 | |
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| 101 | |
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| 102 | Additional information |
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| 103 | ---------------------- |
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| 104 | |
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| 105 | * See arb_INSTALL.txt for additional software needed and/or useful |
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| 106 | together with ARB. |
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| 107 | |
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| 108 | |
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| 109 | PT_server |
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| 110 | --------- |
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| 111 | |
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| 112 | To Install 'ARB' you have to know that some modules use a so |
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| 113 | called 'pt_server' (prefix tree server). |
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| 114 | |
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| 115 | ARB needs a writeable directory to store the pt_server files. |
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| 116 | Those files are needed for fast database search |
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| 117 | (by probe_design, probe_match and the automatic aligner) |
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| 118 | and need a lot of disc space (up to several 100 mega bytes, |
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| 119 | e.g. 4000 16S RNA sequences require about 40 MB). |
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| 120 | This files are not created now. They can be build by any user via |
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| 121 | <ARB_NTREE/Probes/PT_SERVER admin/Build server> |
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| 122 | You may define a special directory as the pt_server files location. |
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| 123 | This prevents any loss of data installing a new version of |
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| 124 | ARB. |
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| 125 | To minimize the use of ressources in a workstation cluster |
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| 126 | only one pt_server for each database is started on a user defined |
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| 127 | host. The first user starts the pt_server, and all other users |
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| 128 | can connect to it. |
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| 129 | |
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| 130 | |
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| 131 | What you should know: Swap |
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| 132 | -------------------------- |
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| 133 | |
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| 134 | Arb needs a lot of virtual memory |
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| 135 | (about 50 Mbyte for 5000 Sequences, Length = 3000). |
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| 136 | You can find out about installed swap space by typing: |
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| 137 | |
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| 138 | Linux 'top' |
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| 139 | SunOS 1.x: 'pstat -s' |
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| 140 | System V / SGI 'swap -s' |
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| 141 | OSF 'swapon -sv' |
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| 142 | |
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| 143 | Call your system administrator or local guru to increase your |
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| 144 | swap. (If you don't have such a nice person, try to read the |
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| 145 | man pages: 'man -k swap') |
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| 146 | |
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| 147 | |
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| 148 | The Database |
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| 149 | ------------ |
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| 150 | |
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| 151 | In the current release a small dataset (demo.arb) is provided. |
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| 152 | This database contains a selection of artificial and real-life |
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| 153 | sequences. |
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| 154 | |
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| 155 | The intention of providing this small dataset first is to give |
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| 156 | you the opportunity to get familiar with the program and to |
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| 157 | test the performance of your computer system as well as the |
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| 158 | stability of ARB on your system. |
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| 159 | |
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| 160 | |
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| 161 | Bugs |
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| 162 | ---- |
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| 163 | |
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| 164 | ARB is running properly and stably on our systems. However, it |
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| 165 | may be that there are bugs never detected by us or never |
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| 166 | appearing on our systems. Please don't hesitate to inform us |
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| 167 | about any bugs. A detailed description of the steps performed |
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| 168 | before the problem was evident and of the number and types of |
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| 169 | modules running at the same time would be extremely helpful to |
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| 170 | our computer scientists. |
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| 171 | |
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| 172 | Please report bugs into our bug tracker at |
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| 173 | http://bugs.arb-home.de/ |
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| 174 | |
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| 175 | |
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| 176 | Support |
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| 177 | ------- |
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| 178 | |
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| 179 | Please send any comments, bug reports or questions to |
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| 180 | |
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| 181 | arb@arb-home.de |
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| 182 | |
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| 183 | |
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| 184 | Copyright Notice |
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| 185 | ---------------- |
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| 186 | |
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| 187 | Please see the file |
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| 188 | |
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| 189 | arb_LICENSE.txt |
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| 190 | |
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| 191 | in the ARB installation directory. |
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| 192 | |
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| 193 | |
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| 194 | Disclaimer |
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| 195 | ---------- |
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| 196 | |
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| 197 | THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED |
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| 198 | FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT |
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| 199 | NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF |
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| 200 | FITNESS FOR A PARTICULAR PURPOSE. |
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| 201 | |
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| 202 | |
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| 203 | Have fun! |
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| 204 | |
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| 205 | |
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