act_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 comparison viewer based on <ULINK
URL="http://www.sanger.ac.uk/resources/software/artemis/"
type="external">Artemis</ULINK>.  The name &prog; stands for Artemis
Comparison Tool.  &prog; is written in Java, reads EMBL or GENBANK format
sequences and feature tables, and can work on sequences of any size.
    </PARA>

    <PARA>
&prog; understands several different comparison file formats.  See <XREF
LINKEND="COMPARISON-RUN"> for details.  Note that &prog; is a comparison
viewer only.  The comparison information itself must be generated externally.
See <XREF LINKEND="COMPARISON-RUN"> for more details.
    </PARA>

    <PARA>
For other information see the <ULINK
URL="http://www.sanger.ac.uk/resources/software/act/" TYPE="external">the &prog; web
pages</ULINK> or the <ULINK
URL="http://www.sanger.ac.uk/resources/software/artemis/" TYPE="external">the &art; 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/act/">&prog; web pages</ULINK>.
    </PARA>

&gettingjava;

    <SECT2 ID="UNIXINSTALLATION">
      <TITLE>Installation Instructions for UNIX and GNU/Linux</TITLE>
      <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.  Uncompress and
untar the <LITERAL>act_compiled.tar.gz</LITERAL> file.  The command
is:
      </PARA>
      <PARA>
         <COMMAND>
tar zxf act_compiled.tar.gz
         </COMMAND>
      </PARA>
      <PARA>
This will create a directory called <LITERAL>~/act</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 1.5 or higher), installing &prog;
is as simple as downloading the the act.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 act.zip, if it does rename it to act.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>

&concepts;

  <SECT1 ID="CONTRIBUTIONS">
    <TITLE>Contributions and Suggestions</TITLE> 
    <PARA> 
We welcome contributions to &prog; and to &art;, 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>