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    <CHAPTER ID="START">
      <TITLE>Starting &prog;</TITLE>
    
      <SECT1 ID="RUNNINGUNIX"> 
        <TITLE>Running &prog; on UNIX and GNU/Linux Systems</TITLE>
        <PARA>
    On Unix and GNU/Linux the easiest way to run the program is to run the script
    called <COMMAND>art</COMMAND> in the &prog; installation directory (see <XREF
    LINKEND="INSTALLATION">) like this:
        </PARA>
    
        <PARA>
          <COMMAND>artemis/art</COMMAND>
        </PARA>
    
        <PARA>
    If all goes well you will be presented with a small window with two
    menus.  See <XREF LINKEND="LAUNCH-WINDOW"> to find out what to do next.
        </PARA>
    
        <PARA>
    Alternatively you start &prog; with the name of a sequence file or embl file
    eg:
        </PARA>
    
        <PARA>
          <COMMAND>artemis/art artemis/etc/c1215.embl</COMMAND>
        </PARA>
    
        <PARA>
    Or if you have a sequence file and extra feature table files you can read
    them all with a command like this (the example file c1215.blastn.tab is the
    result of a BLASTN search against EMBL which has been converted to feature
    table format):
        </PARA>
    
        <PARA>
          <COMMAND>
    artemis/art artemis/etc/c1215.embl + artemis/etc/c1215.blastn.tab
          </COMMAND> 
        </PARA>
        <PARA>
    Note that any number of feature files can be read by listing them after the
    plus sign.  The "+" must be surrounded by spaces.
        </PARA>
    
        <PARA>
    See <XREF LINKEND="UNIXARGS"> for a list of the other possible arguments.
        </PARA>
    
        <PARA>
    Here is an alternative way to run &prog; if the <COMMAND>art</COMMAND> script
    doesn't work for you:
        </PARA>
    
        <PARA>
          <COMMAND>
    cd ~/artemis
          </COMMAND>
        </PARA>
    
        <PARA>
          <COMMAND>
    
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    java -classpath .:./lib/biojava.jar:./lib/jakarta-regexp-1.2.jar:./lib/jemAlign.jar -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain
    
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          </COMMAND>
        </PARA>
      </SECT1>
    
    &unixargs;
    
      <SECT1 ID="RUNNINGMAC">
        <TITLE>Running &prog; on Macintosh Systems</TITLE>
        <PARA>
    On Macintosh machines &prog; can be started by double clicking on the Artemis
    icon.
        </PARA>
      </SECT1>
    
      <SECT1 ID="RUNNINGPC">
        <TITLE>Running &prog; on Windows Systems</TITLE>
        <PARA>
    
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    On systems with Java 1.3 (or above) installed &prog; can be
    
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    started by double clicking on the artemis.jar icon.
        </PARA>
      </SECT1>
    
      <SECT1 ID="LAUNCH-WINDOW">
        <TITLE>The &prog; Launch Window</TITLE>
        <PARA>
    This is the first window that opens when you start &prog;.  The menus at the
    top of this window allow you to read a new sequence or embl entry.
        </PARA>
        <SECT2 ID="LAUNCH-WINDOW-FILE-MENU">
          <TITLE>The File Menu</TITLE>
    
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          <SECT3 ID="LAUNCH-WINDOW-FILEMANAGER">
            <TITLE>Open File Manager ...</TITLE>
            <PARA>
    Selecting this shows the files and directories that are in the directory &prog;
    is launched in. At the top are 2 shortcut buttons to go up a directory and to go 
    to your home directory. At the bottom of the file manager is a file filter.
    You can select a file and double click on it to launch artemis.
            </PARA>
          </SECT3>
    
    
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          <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-OPEN">
            <TITLE>Open ...</TITLE>
            <PARA>
    If you select this menu item a file requester will be displayed which allows
    you to open a flat file containing an entry.  If the file you select is
    successfully read a new window will open, which shows the sequence and
    features for the entry.  See <XREF LINKEND="MAINWINDOW-CHAPTER"> to find out
    how to use the main window.
            </PARA>
          </SECT3>
    
          <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-READ-FROM-EBI">
    
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            <TITLE>Open from EBI - Dbfetch ...</TITLE>
    
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            <PARA>
    The functions will ask the user for an accession number and then will attempt
    to read it directly from the <ULINK URL="http://www.ebi.ac.uk"
    
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    TYPE="external">EBI</ULINK> using 
    <ULINK URL="http://www.ebi.ac.uk/cgi-bin/dbfetch" TYPE="external">Dbfetch</ULINK>.  
    If all goes well you will be presented with an view/edit window (see <XREF
    
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    LINKEND="MAINWINDOW-CHAPTER">).
            </PARA>
            <PARA>
          </SECT3>
    
          <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-QUIT">
            <TITLE>Quit</TITLE>
            <PARA>
    This menu item will close all windows and then exit the program
            </PARA>
          </SECT3>
        </SECT2>
    
    &options-menu;
      </SECT1>
    </CHAPTER>