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>