Welcome to the 'ARB' Sequence Database Tools System Requirements ------------------- ARB is currently developed on Linux PCs only. Compiling ARB using the gcc compiler (versions 2.95.3, 3.x and 4.x series) as well works on Mac OSX and Sun OS - but we do not publish or support these versions. Hardware Requirements (Linux): Good We use Real memory : 1 Gb 4 Gb Free discspace : 1 Gb more Computer speed : 2 GHz Cpu 2 GHz Dual Cpu Note : Memory is more important than a fast processor! Files needed to install ARB --------------------------- File 'arb_install.sh' // install script 'arb.*.tgz' // ARB program Available ARB versions: 'arb.32.*.tgz' // 32 bit versions 'arb.64.*.tgz' // 64 bit versions 'arb.*.SuSE*.tgz // SuSE version 'arb.*.Ubuntu*.tgz // Ubuntu version (recommended) 'arb.*.OPENGL.tgz' // OPENGL version (contains RNA3D, a 3D-molecule-viewer) Choose a 32-bit-version, if your system is 32-bit, choose a 64-bit-version, if your system is 64-bit. Normally one of the Ubuntu versions should work for you, only use one of the SuSE versions, if the Ubuntu version has problems (e.g. does not display group names in ARB_EDIT4). Install/Update ARB ------------------ ARB consists of more than 1200 files which are installed into a single directory. Creating this directory, copying all data into it, and setting the permissions correctly is done by the installation script 'arb_install.sh' Goto the directory, where the files 'arb_install.sh' // install script 'arb_README.txt' // this file 'arb.*.tgz' // ARB binaries are located and type '/bin/sh arb_install.sh' Answer all questions asked by the script. Notes:- The script will ask about a pt_server directory. This is a directory where arb will store big index files. You should enter a different path as you do not want to recreate those files after an ARB update. - Normally pressing enter will be a good choice. - You can rerun the script many times, it can be used to change an existing installation. Change your .cshrc/.profile files: Set the environment variable ARBHOME to the ARB installation directory Append $ARBHOME/bin to your PATH reread it, (logout+login ) goto a directory with a demo database 'eg demo.arb' and start 'ARB' with 'arb' Additional information ---------------------- * See arb_INSTALL.txt for additional software needed and/or useful together with ARB. PT_server --------- To Install 'ARB' you have to know that some modules use a so called 'pt_server' (prefix tree server). ARB needs a writeable directory to store the pt_server files. Those files are needed for fast database search (by probe_design, probe_match and the automatic aligner) and need a lot of disc space (up to several 100 mega bytes, e.g. 4000 16S RNA sequences require about 40 MB). This files are not created now. They can be build by any user via You may define a special directory as the pt_server files location. This prevents any loss of data installing a new version of ARB. To minimize the use of ressources in a workstation cluster only one pt_server for each database is started on a user defined host. The first user starts the pt_server, and all other users can connect to it. What you should know: Swap -------------------------- Arb needs a lot of virtual memory (about 50 Mbyte for 5000 Sequences, Length = 3000). You can find out about installed swap space by typing: Linux 'top' SunOS 1.x: 'pstat -s' System V / SGI 'swap -s' OSF 'swapon -sv' Call your system administrator or local guru to increase your swap. (If you don't have such a nice person, try to read the man pages: 'man -k swap') The Database ------------ In the current release a small dataset (demo.arb) is provided. This database contains a selection of artificial and real-life sequences. The intention of providing this small dataset first is to give you the opportunity to get familiar with the program and to test the performance of your computer system as well as the stability of ARB on your system. Bugs ---- ARB is running properly and stably on our systems. However, it may be that there are bugs never detected by us or never appearing on our systems. Please don't hesitate to inform us about any bugs. A detailed description of the steps performed before the problem was evident and of the number and types of modules running at the same time would be extremely helpful to our computer scientists. Please report bugs into our bug tracker at http://bugs.arb-home.de/ Support ------- Please send any comments, bug reports or questions to arb@arb-home.de Copyright Notice ---------------- Please see the file arb_LICENSE.txt in the ARB installation directory. Disclaimer ---------- THE AUTHORS OF ARB GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. Have fun!