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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>
java -classpath .:./lib/biojava.jar:./lib/jakarta-regexp-1.2.jar:./lib/jemAlign.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 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>
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-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>
<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">
<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>