3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Running Jalview from the command line</title>
27 <strong>Running Jalview from the command line</strong>
30 Jalview can be run from the command line, and provides a <a
31 href="clarguments.html">range of arguments</a>.
33 <p>There are a few different ways to do this:</p>
35 <li>Use the <strong>jalview</strong> command that links to a <strong>launch
36 script</strong>. Launch scripts are available if you are running an up to
37 date version of Jalview (at least 2.11.2.0), or have installed
38 Jalview via a package manager (e.g. conda, homebrew, apt).
40 <li>Embed arguments in a <strong>.JVL</strong> file. These
41 files will be opened automatically by the Jalview application when
42 double-clicked in a file browser on Windows and OSX.
44 <li>Execute the Jalview standalone Jar file with an existing
45 Java installation</li>
46 <li>For older versions of Jalview, call the <a href="#olderinstalls">native launch program directly</a>.
49 <strong><a name="script">Jalview's command line launch
51 <p>Since version 2.11.2, the Jalview native application includes a <strong>launching shell script</strong>. This is the easiest way to
52 launch an installed Jalview application from the command line. </p><p>To run the <strong>launch script</strong>, simply open a Terminal (or Command prompt on Windows), and type:<pre>
56 <p>There are some important differences between the using the launching script and launching Jalview from its icon:
59 <li>The launching script will NOT perform automatic updates.</li>
60 <li>The launching script cannot open or use JVL files.</li>
63 <em><strong>Adding the launch script to your path</strong></em>
65 If typing 'jalview' in the terminal prompt (or windows command line)
66 doesn't work then you will need to add the location of the jalview
68 <code>PATH</code>.</p><p>
69 How you do this depends on your operating system.
75 <p><em>In <strong>Linux</strong> or <strong>Unix</strong> (<code>jalview.sh</code>)</em></p>
76 <p>Running the Linux installer will give you the option of adding a symbolic link to
77 that script in your <code>$PATH</code>, if it finds a suitable place that your user can add such a
78 link (e.g. <code>~/bin</code>, <code>~/.local/bin</code>, <code>~/local/bin</code>, <code>~/opt/bin</code>). If you chose that option then
79 you should be able to launch Jalview on the command line with the simple command
81 If you didn't choose that option during installation (or used an earlier version installer), or wish to make another symbolic link, you can link to the
82 launching shell script with the command
83 <pre>ln -s /PATH_TO_JALVIEW/bin/jalview.sh jalview</pre>
84 or you could add <code>/PATH_TO_JALVIEW/bin</code> to your own <code>$PATH</code> as it already contains a symbolic link <code>jalview</code>.
88 <p><em>In <strong>Windows</strong> (<code>jalview.bat</code>, <code>jalview.ps1</code>)</em></p>
89 <p>The Windows installer will give you the option of adding Jalview's script folder to your <code>%PATH%</code> allowing you to launch Jalview
90 in a Command Prompt simply with the command
92 If you didn't choose that option during installation (or used an earlier version installer), you can either
96 add the <code>\PATH_TO_JALVIEW\bin</code> folder to your <code>%PATH%</code>, or
99 run the launcher script on the command line with its full path
100 <pre>\PATH_TO_JALVIEW\bin\jalview.bat</pre>
101 (you can leave off the <code>.bat</code> extension if you want).
104 The <code>jalview.bat</code> file is a generic wrapper around the
105 PowerShell script <code>jalview.ps1</code> in the same folder. This PowerShell script should work with both
106 PowerShell 5.x (which is installed by default on all modern Windows machines), and also PowerShell 6.0+
107 which might have been installed afterwards.
111 <p><em>In <strong>macOS</strong> (<code>jalview</code>)</em></p>
113 We don't currently provide a macOS installer program, so you will need to add the command to you path manually. The script you should use to launch Jalview is linked to as
114 <pre>/Applications/Jalview.app/Contents/MacOS/jalview</pre>
115 so you can run that command with its full path, or make your own symbolic link to there, or add that folder to your <code>$PATH</code>.
118 If you cannot see the
120 command in the MacOS directory, then you probably have an older
121 Jalview installation. In that case, you should make a symbolic
122 link directly to the launch script with the command
123 <pre>ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview</pre>
124 <em>If this doens't work, check your installation is running
125 Jalview 2.11.2.0 or later.</em>
129 <!-- <p><em>Future</em></p>
130 A future version of Jalview will include a tool to allow adding these "<code>jalview</code>" links to your <code>PATH</code> automatically.
135 <p><strong><a name="olderinstalls">Older versions of Jalview</a></strong></p>
138 If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to
139 use a more platform specific way to launch and use command line arguments.
142 <li>Standard installation on Linux/Unix:
143 <pre>/PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
145 <li>Standard installation on Windows:
146 <pre>\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
149 <pre>open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa</pre>
150 <em>(put all the Jalview arguments <em>after</em> the --args parameter, and note that <strong>all files must be specified with their full paths</strong>)</em>
153 <li>Jalview standalone executable Jar<pre>
154 <Path to Java home>/bin/java -jar <Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa</pre></li>
157 If you have installed Jalview via <em>conda</em> or another package
158 manager then you most likely have a 'jalview' command available in
159 your terminal shell's default path. Alternately, if you have built
160 Jalview from source, then take a look at the doc/building.md file
161 included in the source distribution.
164 Use '-help' to get more information on the <a
165 href="clarguments.html">command line arguments</a> that Jalview
169 <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
170 to modify parameters for Jalview's Java Virtual Machine, or
171 configure system properties, then take a look at the instructions
172 for how to <a href="../memory.html#jvm">setting the JVM's
173 maximum memory</a>.<br />
175 <strong>Changing Jalview's 'Look and Feel'</strong> <br />If you
176 are experiencing issues with the font size or layout of Jalview's
177 GUI, you can try changing Jalview's 'Look and feel' by
178 specifying a custom system property 'laf' on startup (see <a
179 href="../memory.html#jvm">setting the JVM's memory</a> for
180 instructions on how to do this for your platform). <br />For the
181 Jalview standalone executable jar, simply provide one of the
182 property settings before the -jar argument
185 <li>-Dlaf=system (default look and feel for the OS)</li>
186 <li>-Dlaf=crossplatform (Java's Metal Look and Feel)</li>
187 <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
188 <li>-Dlaf=mac (only has an effect on OSX)</li>
189 <li>-Dlaf=gtk (only has an effect on Linux)</li>
190 <li>-Dlaf=metal (force Java's Metal Look and Feel, default on linux)</li>
191 <li>-Dlaf=quaqua (macOS only. Force attempt at old macOS theme)</li>
192 <li>-Dlaf=vaqua (macOS only. Force attempt at modern macOS theme)</li>
194 The currently configured look and feel is logged to Jalview's console.
195 Once the look and feel has been changed, it will be stored in
196 Jalview's .jalview_properties file for future Jalview sessions. This property is <strong>PREFERRED_LAF</strong> and can also be used to set the Look and feel by editing your .jalview_properties file.