3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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>. These arguments
32 can also be passed via <strong>.JVL</strong> files, which are opened
33 automatically by the Jalview application when double-clicked in a
34 file browser on Windows and OSX.
36 The way that you launch Jalview from the command line depends on the
37 platform you are on, and how it has been installed.
40 <li>Standard installation on Linux/Unix:<pre>
41 /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
43 <li>Standard installation on Windows:<pre>
44 \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
46 <li>OSX Application:<pre>
47 open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
48 all the Jalview arguments <em>after</em> the --args parameter)
51 <li>Jalview standalone executable Jar<pre>
52 <Path to Java home>/bin/java -jar <Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa</pre></li>
55 If you have installed Jalview via <em>conda</em> or another package
56 manager then you most likely have a 'jalview' command available in
57 your terminal shell's default path. Alternately, if you have built
58 Jalview from source, then take a look at the doc/building.md file
59 included in the source distribution.
62 Use '-help' to get more information on the <a
63 href="clarguments.html">command line arguments</a> that Jalview
67 <strong>Passing JVM Arguments to Jalview</strong><br /> If you need
68 to modify parameters for Jalview's Java Virtual Machine, then take a
69 look at the instructions for how to <a href="../memory.html#jvm">setting
70 the JVM's maximum memory</a>.