intro_chapter.sgml

<CHAPTER ID="INTRODUCTION">
  <TITLE>Introduction to &prog;</TITLE>
  
  <SECT1 ID="WHATIS">
    <TITLE>What is &prog;?</TITLE>
    <PARA>
  &prog; is a DNA sequence viewer and annotation tool that allows visualisation
of sequence features and the results of analyses within the context of the
sequence, and its six-frame translation.  &prog; is written in Java, reads
EMBL or GENBANK format sequences and feature tables, and can work on sequences
of any size.
    </PARA>

    <PARA>
On Unix and GNU/Linux systems, given an EMBL accession number &prog; also can
read an entry 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>.  This
feature is still experimental, but copes well with straightforward entries
(see <XREF LINKEND="LAUNCH-WINDOW-FILE-MENU-READ-FROM-EBI">).
    </PARA>

    <PARA>
For more information on &prog; go to 
<ULINK URL="http://www.sanger.ac.uk/resources/software/artemis/" TYPE="external">the &prog;
web pages</ULINK>.
    </PARA>
  </SECT1>

&requirements;

  <SECT1 ID="INSTALLATION">
    <TITLE>Getting and Installing &prog;</TITLE>
    <PARA>
The most up to date version of &prog; is always available from the <ULINK
URL="http://www.sanger.ac.uk/resources/software/artemis/">&art; web pages</ULINK>.
    </PARA>

&gettingjava;

    <SECT2 ID="UNIXINSTALLATION">
      <TITLE>Installation Instructions for UNIX and GNU/Linux</TITLE>
      <PARA>
        <ITEMIZEDLIST>
          <LISTITEM>
            <PARA>
Change directory to the directory you wish to install &prog; in.  We will use
<LITERAL>~/</LITERAL> in this example and in the next chapter.
            </PARA>
          </LISTITEM>
          <LISTITEM>
            <PARA>
uncompress and untar the <LITERAL>artemis_compiled.tar.gz</LITERAL> file.  On
UNIX the command is:
            </PARA>
            <PARA>
              <COMMAND>
tar zxf artemis_compiled.tar.gz
              </COMMAND>
            </PARA>
          </LISTITEM>
        </ITEMIZEDLIST>
This will create a directory called <LITERAL>~/artemis</LITERAL> which will
contain all the files necessity for running &prog;.
      </PARA>
  
      <PARA>
For instructions on how to run &prog; on UNIX and GNU/Linux once the archive
is unpacked see <XREF LINKEND="RUNNINGUNIX">.
      </PARA>
    </SECT2>

    <SECT2 ID="MACINSTALLATION">
      <TITLE>Installation Instructions for MacOSX</TITLE>
      <PARA>
For MacOSX users an archive artemis_act.dmg.gz disk image is provided.
This contains both Artemis and ACT applications.
This can be uncompressed using gunzip:
      </PARA>
      <PARA>
<ComputerOutput>gunzip artemis_act.dmg.gz</ComputerOutput>
      </PARA>
      <PARA>
Alternatively on OS X an easier solution is provided by StuffIt Expander.
Double-click on any file ending in ".gz" and StuffIt Expander will be
launched to uncompress that file. 

<MEDIAOBJECT>
<IMAGEOBJECT>
   <IMAGEDATA FORMAT="gif" FILEREF="mac_osx_dmg.gif">
            </IMAGEOBJECT>
</MEDIAOBJECT>

The uncompressed disk image file "artemis_act.dmg" can be mounted by double 
clicking on it. The mounted image, "artemis_act", can then be opened 
and the software contents displayed by double clicking on it. Open an read the 
"Readme.txt" file.
        </PARA>
    </SECT2>

    <SECT2 ID="DOSINSTALLATION">
      <TITLE>Installation Instructions for Windows</TITLE>
      <PARA>
On Windows systems with Java (version 1.6 or higher), installing &prog; 
is as simple as downloading the the artemis.jar file to an appropriate 
place (such as the desktop or the Programs folder). When downloading
some versions of windows mistake this file for a zip file ensure it
does not name this artemis.zip, if it does rename it to artemis.jar 
(DO NOT UNZIP THIS FILE).
      </PARA>

      <PARA>
For instructions on how to run &prog; on Windows once it is unpacked see <XREF
LINKEND="RUNNINGPC"> .
      </PARA>
    </SECT2>
  </SECT1>

&filetypes;
&concepts;

  <SECT1 ID="CONTRIBUTIONS">
    <TITLE>Contributions and Suggestions</TITLE> 
    <PARA> 
We welcome contributions to &prog;, bug reports from users and suggestions for
new features.  An email discussion list has been set up for this purpose.  To
join, send a message to 'artemis-users-join@sanger.ac.uk' with 'subscribe
artemis-users' in the body (not the subject).  Announcements will also be sent
to this list.
    </PARA>
  </SECT1>

&acknowledgments;

&copyright;

</CHAPTER>