1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
|
<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;
©right;
</CHAPTER>
|
