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://corba.ebi.ac.uk/index.html" TYPE="external">CORBA</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 go to <ULINK 
URL="http://www.sanger.ac.uk/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/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>
gzip -d &lt; artemis_compiled.tar.gz | tar xf -
              </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 Macintosh Systems</TITLE>
      <PARA>
Macintosh users should download and run the <LITERAL>Artemis.bin</LITERAL>
file from the <ULINK URL="http://www.sanger.ac.uk/Software/Artemis">&art; web
pages</ULINK>, which will create a local copy of the the &art; application
(along with an icon).
      </PARA>

      <SECT3 ID="MACINSTALLATION-OSX">
        <TITLE></TITLE>
        <PARA>
Notes from Carton Chen &lt;cwchen@ym.edu.tw&gt;
          <SYNOPSIS>
Running Artemis under Mac OSX
(using Artemis v. 5 beta as example)

Mac OS X is built on Unix, and therefore there is no reason why Unix version
of Artemis, written in Java, cannot be made to run under this operation
system. We have discovered a rather simple procedure to set it up so that
Artemis will come alive upon a double click. Below is a step-by-step guide
using the newest Artemis version (v. 5 beta) as example. Procedures for
other versions should be pretty much the same.

Down load 'artemis_compiled_v5.tar.gz' from
ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/v5/

Place the downloaded original file into Applications subdirectory
    [Note: Do not use Stuffit Expander to decompress the file. If your ftp
program automatically uses Stuffit Expander to decompress downloaded files,
turn if off, or simply make sure that you move the original file (not the
decompressed file) here. This is because somehow Stuffit Expander limited
file names to 31 characters, and therefore files with longer names cannot be
found by the program during execution].

Go to Terminal and go to the Applications subdirectory by typing:
    cd /Applications/

Decompress the file by typing:
    tar zxvf [file name]

A new subdirectory 'artemis' will be created. Delete the downloaded file,
and go to the artemis subdirectory by typing:
    cd artemis

Now you can execute artemis right there by typing
    ./art
    (Don't overlook the period!)

For ultimate convenience, you want to be able to start Artemis right from
the Finder without getting into Terminal. To do that, quit Terminal and go
to the artemis subdirectory (under Applications) in the Finder, and change
the file name 'art' to 'art.command'.

That's it. Now whenever you double click 'art.command'. It will start
Terminal automatically and present you Artemis right in your face.

Now the question is which should I play with using this fantastic program.

The above procedure has been worked out by my student Chi Chen who may be
contacted at g39008006@ym.edu.tw.

Have fun.
Carton W. Chen
National Yang-Ming Universtiy
Taipei, Taiwan
cwchen@ym,edu.tw
          </SYNOPSIS>
        </PARA>
      </SECT3>
    </SECT2>

    <SECT2 ID="DOSINSTALLATION">
      <TITLE>Installation Instructions for Windows</TITLE>
      <PARA>
On Windows systems with Java (version 1.3 or higher), installing &prog; 
is as simple as copying the
<ULINK URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/artemis.jar"
TYPE="external">artemis.jar file</ULINK> to an appropriate place (such as the
desktop or the Programs folder).
      </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;, 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 'majordomo@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>