start_chapter.sgml

<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 three
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. Also
to see a summary of the options type:
    </PARA>

   <PARA>
      <COMMAND>artemis/art -help</COMMAND>
   </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>
java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain
      </COMMAND>
    </PARA>
  </SECT1>

&unixargs;

  <SECT1 ID="RUNNINGMAC">
    <TITLE>Running &prog; on Macintosh Systems</TITLE>
    <PARA>
On MacOSX machines &prog; can be started by double clicking on the Artemis
icon. The icon can be added to the dock by dragging it from a 'Finder' window
and dropping it onto the position in the dock you want it. In addition
sequence files (with gff, embl, EMBL, genbank, gbk, fasta, seq, art file name
extensions) can be dragged and dropped on to the Artemis application image to 
open them up.
    </PARA>
    <PARA>
To change the memory allocated to &prog; on MacOSX, set the value in the file Info.plist 
in the directory Artemis.app/Contents. Towards the bottom of the file there are a couple of 
lines that look like this:
<SYNOPSIS>
 &lt;key&gt;VMOptions&lt;/key&gt;
 &lt;string&gt;-Xmx800m&lt;/string&gt;
</SYNOPSIS>
 Changing the value after -Xmx will change the memory used by &prog;. 
    </PARA>
  </SECT1>

  <SECT1 ID="RUNNINGPC">
    <TITLE>Running &prog; on Windows Systems</TITLE>
    <PARA>
On systems with Java 1.6 (or above) installed &prog; can be
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>

      <SECT3 ID="LAUNCH-WINDOW-PROJMANAGER">
        <TITLE>Open Project Manager ...</TITLE>
        <PARA>
This opens up the Project File Manager which can be used to facilitate launching
of groups of files (annotation, userplot, BAM, VCF) with a particular sequence.
See <XREF LINKEND="PROJ-MANAGER-CHAPTER">.
        </PARA>
      </SECT3>

      <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 from. The user home directory and the current working directories
are shown and can be navigated. 
        </PARA>
      </SECT3>

      <SECT3 ID="LAUNCH-WINDOW-SSH-FILEMANAGER">
        <TITLE>Open SSH File Manager ...</TITLE>
        <PARA>
This opens a window displaying a local file manager at the top and login
options to access a remote file system via Secure Shell (SSH). When the
login details are typed in and 'Connect' pressed the bottom half of the 
window will display the other (remote) file system. See <XREF LINKEND="SSH-CHAPTER"> 
to find out how to use this and how to set up the connection.
        </PARA>
      </SECT3>


      <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">
        <TITLE>Open from EBI - Dbfetch ...</TITLE>
        <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"
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
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>