| 1 | |
|---|
| 2 | Welcome to the 'ARB' Sequence Database Tools |
|---|
| 3 | |
|---|
| 4 | |
|---|
| 5 | System Requirements |
|---|
| 6 | ------------------- |
|---|
| 7 | |
|---|
| 8 | |
|---|
| 9 | ARB is currently developed for Linux and OSX. |
|---|
| 10 | |
|---|
| 11 | Hardware Requirements (Linux): |
|---|
| 12 | |
|---|
| 13 | Good We use |
|---|
| 14 | Real memory : 1 Gb 4 Gb |
|---|
| 15 | Free discspace : 1 Gb more |
|---|
| 16 | Computer speed : 2 GHz Cpu 2 GHz Dual Cpu |
|---|
| 17 | |
|---|
| 18 | |
|---|
| 19 | Note : Memory is more important than a fast processor! |
|---|
| 20 | |
|---|
| 21 | |
|---|
| 22 | Files needed to install ARB |
|---|
| 23 | --------------------------- |
|---|
| 24 | |
|---|
| 25 | File |
|---|
| 26 | |
|---|
| 27 | 'arb_install.sh' // install script |
|---|
| 28 | 'arb-*.tgz' // ARB program |
|---|
| 29 | |
|---|
| 30 | |
|---|
| 31 | Available ARB versions: |
|---|
| 32 | |
|---|
| 33 | arb-*.centos5-amd64.tgz |
|---|
| 34 | arb-*.centos6-amd64.tgz |
|---|
| 35 | arb-*.ubuntu1004-amd64.tgz |
|---|
| 36 | arb-*.ubuntu1204-amd64.tgz |
|---|
| 37 | arb-*.ubuntu1304-amd64.tgz |
|---|
| 38 | arb-*.osx.tgz |
|---|
| 39 | |
|---|
| 40 | You need exactly ONE of the available 'arb-*.tgz'! |
|---|
| 41 | |
|---|
| 42 | Notes: |
|---|
| 43 | |
|---|
| 44 | * all versions are 64bit versions |
|---|
| 45 | (if you really need a 32bit version, see http://download.arb-home.de/release/arb_5.5/) |
|---|
| 46 | |
|---|
| 47 | * all versions are compiled without OPENGL |
|---|
| 48 | (if you rely on OPENGL features, either stick with arb_5.5 or compile arb from source) |
|---|
| 49 | |
|---|
| 50 | * OSX version is available as arb-*.osx.tgz |
|---|
| 51 | and via MacPorts (see arb_OS_X_MacPorts.txt included inside arb-*.osx.tgz) |
|---|
| 52 | |
|---|
| 53 | * debian users should either use the arb package in 'non-free' or |
|---|
| 54 | install one of the centos versions (see also arb_INSTALL.txt) |
|---|
| 55 | |
|---|
| 56 | |
|---|
| 57 | Install/Update ARB |
|---|
| 58 | ------------------ |
|---|
| 59 | |
|---|
| 60 | ARB consists of more than 1400 files which are installed into a single |
|---|
| 61 | directory. Creating this directory, copying all data into it, and setting |
|---|
| 62 | the permissions correctly is done by the installation script |
|---|
| 63 | |
|---|
| 64 | 'arb_install.sh' |
|---|
| 65 | |
|---|
| 66 | Open a terminal, change to the directory where you have saved the |
|---|
| 67 | files needed for installation: |
|---|
| 68 | |
|---|
| 69 | 'arb_install.sh' // install script |
|---|
| 70 | 'arb_README.txt' // this file |
|---|
| 71 | 'arb-*.tgz' // your chosen ARB version |
|---|
| 72 | |
|---|
| 73 | |
|---|
| 74 | and type |
|---|
| 75 | |
|---|
| 76 | '/bin/sh arb_install.sh' |
|---|
| 77 | |
|---|
| 78 | (to install arb for all users call the script as root or via sudo) |
|---|
| 79 | |
|---|
| 80 | |
|---|
| 81 | Answer all questions asked by the script. |
|---|
| 82 | |
|---|
| 83 | Notes:- The script will ask about a pt_server directory. This is a |
|---|
| 84 | directory where arb will store big index files. |
|---|
| 85 | You should enter a different path as you do not want to |
|---|
| 86 | recreate those files after an ARB update. |
|---|
| 87 | - Normally pressing enter will be a good choice. |
|---|
| 88 | - You can rerun the script many times, it can be used to |
|---|
| 89 | change an existing installation. |
|---|
| 90 | |
|---|
| 91 | Change your .cshrc/.profile files: |
|---|
| 92 | |
|---|
| 93 | Set the environment variable ARBHOME |
|---|
| 94 | to the ARB installation directory |
|---|
| 95 | Append $ARBHOME/bin to your PATH |
|---|
| 96 | |
|---|
| 97 | reread it, (logout+login) |
|---|
| 98 | |
|---|
| 99 | goto a directory with a demo database 'eg demo.arb' |
|---|
| 100 | and start 'ARB' with |
|---|
| 101 | |
|---|
| 102 | 'arb' |
|---|
| 103 | |
|---|
| 104 | Compile ARB from source |
|---|
| 105 | ----------------------- |
|---|
| 106 | |
|---|
| 107 | * See arb_INSTALL.txt for information about how to compile |
|---|
| 108 | arb from source. |
|---|
| 109 | |
|---|
| 110 | |
|---|
| 111 | Additional information |
|---|
| 112 | ---------------------- |
|---|
| 113 | |
|---|
| 114 | * See arb_INSTALL.txt for additional software needed and/or useful |
|---|
| 115 | together with ARB. |
|---|
| 116 | |
|---|
| 117 | |
|---|
| 118 | PT_server |
|---|
| 119 | --------- |
|---|
| 120 | |
|---|
| 121 | To Install 'ARB' you have to know that some modules use a so |
|---|
| 122 | called 'pt_server' (prefix tree server). |
|---|
| 123 | |
|---|
| 124 | ARB needs a writeable directory to store the pt_server files. |
|---|
| 125 | Those files are needed for fast database search |
|---|
| 126 | (by probe_design, probe_match and the automatic aligner) |
|---|
| 127 | and need a lot of disc space (up to several 100 mega bytes, |
|---|
| 128 | e.g. 4000 16S RNA sequences require about 40 MB). |
|---|
| 129 | This files are not created now. They can be build by any user via |
|---|
| 130 | <ARB_NTREE/Probes/PT_SERVER admin/Build server> |
|---|
| 131 | You may define a special directory as the pt_server files location. |
|---|
| 132 | This prevents any loss of data installing a new version of |
|---|
| 133 | ARB. |
|---|
| 134 | To minimize the use of ressources in a workstation cluster |
|---|
| 135 | only one pt_server for each database is started on a user defined |
|---|
| 136 | host. The first user starts the pt_server, and all other users |
|---|
| 137 | can connect to it. |
|---|
| 138 | |
|---|
| 139 | |
|---|
| 140 | What you should know: Swap |
|---|
| 141 | -------------------------- |
|---|
| 142 | |
|---|
| 143 | Arb needs a lot of virtual memory |
|---|
| 144 | (about 50 Mbyte for 5000 Sequences, Length = 3000). |
|---|
| 145 | You can find out about installed swap space by typing: |
|---|
| 146 | |
|---|
| 147 | Linux 'top' |
|---|
| 148 | SunOS 1.x: 'pstat -s' |
|---|
| 149 | System V / SGI 'swap -s' |
|---|
| 150 | OSF 'swapon -sv' |
|---|
| 151 | |
|---|
| 152 | Call your system administrator or local guru to increase your |
|---|
| 153 | swap. (If you don't have such a nice person, try to read the |
|---|
| 154 | man pages: 'man -k swap') |
|---|
| 155 | |
|---|
| 156 | |
|---|
| 157 | The Database |
|---|
| 158 | ------------ |
|---|
| 159 | |
|---|
| 160 | In the current release a small dataset (demo.arb) is provided. |
|---|
| 161 | This database contains a selection of artificial and real-life |
|---|
| 162 | sequences. |
|---|
| 163 | |
|---|
| 164 | The intention of providing this small dataset first is to give |
|---|
| 165 | you the opportunity to get familiar with the program and to |
|---|
| 166 | test the performance of your computer system as well as the |
|---|
| 167 | stability of ARB on your system. |
|---|
| 168 | |
|---|
| 169 | |
|---|
| 170 | Bugs |
|---|
| 171 | ---- |
|---|
| 172 | |
|---|
| 173 | ARB is running properly and stably on our systems. However, it |
|---|
| 174 | may be that there are bugs never detected by us or never |
|---|
| 175 | appearing on our systems. Please don't hesitate to inform us |
|---|
| 176 | about any bugs. A detailed description of the steps performed |
|---|
| 177 | before the problem was evident and of the number and types of |
|---|
| 178 | modules running at the same time would be extremely helpful to |
|---|
| 179 | our computer scientists. |
|---|
| 180 | |
|---|
| 181 | Please report bugs into our bug tracker at |
|---|
| 182 | http://bugs.arb-home.de/ |
|---|
| 183 | |
|---|
| 184 | |
|---|
| 185 | Support |
|---|
| 186 | ------- |
|---|
| 187 | |
|---|
| 188 | Please send any comments, bug reports or questions to |
|---|
| 189 | |
|---|
| 190 | arb@arb-home.de |
|---|
| 191 | |
|---|
| 192 | |
|---|
| 193 | Copyright Notice |
|---|
| 194 | ---------------- |
|---|
| 195 | |
|---|
| 196 | Please see the file |
|---|
| 197 | |
|---|
| 198 | arb_LICENSE.txt |
|---|
| 199 | |
|---|
| 200 | in the ARB installation directory. |
|---|
| 201 | |
|---|
| 202 | |
|---|
| 203 | Disclaimer |
|---|
| 204 | ---------- |
|---|
| 205 | |
|---|
| 206 | THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED |
|---|
| 207 | FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT |
|---|
| 208 | NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF |
|---|
| 209 | FITNESS FOR A PARTICULAR PURPOSE. |
|---|
| 210 | |
|---|
| 211 | |
|---|
| 212 | Have fun! |
|---|
| 213 | |
|---|
| 214 | |
|---|
