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.
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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.
22 <title>Jalview Command Line Arguments</title>
25 <strong>The Jalview Executable's Command Line Arguments</strong>
28 <a href="commandline.html">running Jalview from the command line</a>
31 <br />Jalview processes arguments on the command line sequentially. If
32 you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
33 <a href="../memory.html">memory settings</a> or any other launch
34 parameters, then include it at the beginning of the command line to
35 ensure they are processed before any remaining arguments.
37 <table width="100%" border="1" cellspacing="0" cellpadding="0">
39 <td width="27%"><div align="center">-nodisplay</div></td>
40 <td width="73%"><div align="left">Run Jalview without
41 User Interface. (automatically disables questionnaire, version
42 and usage stats checks)</div></td>
46 <td><div align="center">-props FILE/URL</div></td>
47 <td><div align="left">Use the given Jalview properties
48 file instead of users default.</div></td>
51 <td><div align="center">-features FILE/URL</div></td>
52 <td><div align="left">
54 Use the given file to add sequence features to an alignment.
55 See <a href="featuresFormat.html" target="NEW">Features
56 File</a> (Known as Groups file prior to 2.08) description.
63 <div align="center">-colour COLOURSCHEME</div>
65 <td>Set the colourscheme for the alignment. This can be any
66 of the built-in colourschemes, a name of a predefined
67 colourscheme (defined in the Jalview properties file), or an
68 'inline' colourscheme (see the applet's colour parameter for
69 more information).</td>
73 <div align="center">-annotations FILE/URL</div>
75 <td>Add precalculated annotations to the alignment. See <a
76 href="annotationsFormat.html" target="NEW">Annotation
82 <div align="center">-tree FILE/URL</div>
84 <div align="left">Load the given newick format tree file
85 onto the alignment</div>
90 <div align="center">-questionnaire URL</div>
92 <div align="left">Queries the given URL for information
93 about any Jalview user questionnaires</div>
98 <div align="center">-noquestionnaire</div>
100 <div align="left">Turn off questionnaire check</div>
105 <div align="center">-nonews</div>
108 Disable check for <a href="../webServices/newsreader.html">Jalview
109 news</a> on startup (not recommended other than for classroom /
116 <div align="center">-nousagestats</div>
118 <div align="left">Turn off google analytics usage tracking</div>
123 <div align="center">-[no]sortbytree</div>
125 <div align="left">Enable or disable automatic sorting of
126 associated view when a new tree is displayed</div>
131 <div align="center">-groovy FILE/URL</div>
133 <div align="left">Execute groovy script in FILE (where
134 FILE may be 'STDIN' to read from the standard input) after all
135 other arguments have been processed</div>
140 <div align="center">-jabaws URL</div>
142 <div align="left">Specify the URL of the preferred JABAWS
148 <div align="center">-fasta FILE</div>
152 <div align="left">Create alignment file FILE in Fasta
157 <td><div align="center">-clustal FILE</div></td>
158 <td><div align="left">Create alignment file FILE in
159 Clustal format.</div></td>
162 <td><div align="center">-msf FILE</div></td>
164 <td><div align="left">Create alignment file FILE in MSF
168 <td><div align="center">-pileup FILE</div></td>
169 <td><div align="left">Create alignment file FILE in
170 Pileup format.</div></td>
173 <td><div align="center">-pir FILE</div></td>
175 <td><div align="left">Create alignment file FILE in PIR
179 <td><div align="center">-pfam FILE</div></td>
180 <td><div align="left">Create alignment file FILE in
181 PFAM format.</div></td>
184 <td><div align="center">-blc FILE</div></td>
185 <td><div align="left">Create alignment file FILE in BLC
189 <td><div align="center">-json FILE</div></td>
190 <td><div align="left">Create alignment file FILE in
191 JSON format.</div></td>
194 <td><div align="center">-jalview FILE</div></td>
196 <td><div align="left">Create alignment file FILE in
197 Jalview format.</div></td>
200 <td><div align="center">-png FILE</div></td>
201 <td><div align="left">Create PNG image FILE from
202 alignment.</div></td>
205 <td><div align="center">-imgMap FILE</div></td>
207 <td><div align="left">Create HTML file FILE with image
208 map of PNG image.</div></td>
211 <td><div align="center">-eps FILE</div></td>
212 <td><div align="left">Create EPS file FILE from
213 alignment.</div></td>
216 <td><div align="center">-svg FILE</div></td>
217 <td><div align="left">Create Scalable Vector Graphics
218 file FILE from alignment.</div></td>
221 <td><div align="center">-biojsMSA FILE</div></td>
222 <td><div align="left">Write an HTML page to display
223 the alignment with the <a href="biojsmsa.html">
224 BioJS MSAviewer MSA</a>
229 <td><div align="center">-jvmmempc=PERCENT</div></td>
230 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
231 Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
232 This defaults to 90 if total physical memory can be detected.
233 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
238 <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
239 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
240 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
241 gigabytes(g) or if you're lucky enough, terabytes(t).
242 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
243 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.