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 Typical command line execution follows the following pattern:
39 jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
42 <table width="100%" border="1" cellspacing="0" cellpadding="0">
44 <td width="27%"><div align="center">-nodisplay</div></td>
45 <td width="73%"><div align="left">Run Jalview without
46 User Interface. (automatically disables questionnaire, version
47 and usage stats checks)</div></td>
50 <td><div align="center">-open FILE/URL</div></td>
51 <td><div align="left">Specify the alignment file to
52 open or process by providing additional arguments.</div></td>
55 <td><div align="center">-props FILE/URL</div></td>
56 <td><div align="left">Use the given Jalview properties
57 file instead of users default.</div></td>
60 <td><div align="center">-features FILE/URL</div></td>
61 <td><div align="left">
63 Use the given file to add sequence features to an alignment.
64 See <a href="featuresFormat.html" target="NEW">Features
65 File</a> (Known as Groups file prior to 2.08) description.
72 <div align="center">-colour COLOURSCHEME</div>
74 <td>Set the colourscheme for the alignment. This can be any
75 of the built-in colourschemes, a name of a predefined
76 colourscheme (defined in the Jalview properties file), or an
77 'inline' colourscheme (see the applet's colour parameter for
78 more information).</td>
82 <div align="center">-annotations FILE/URL</div>
84 <td>Add precalculated annotations to the alignment. See <a
85 href="annotationsFormat.html" target="NEW">Annotation
91 <div align="center">-tree FILE/URL</div>
93 <div align="left">Load the given newick format tree file
94 onto the alignment</div>
99 <div align="center">-questionnaire URL</div>
101 <div align="left">Queries the given URL for information
102 about any Jalview user questionnaires</div>
107 <div align="center">-noquestionnaire</div>
109 <div align="left">Turn off questionnaire check</div>
114 <div align="center">-nonews</div>
117 Disable check for <a href="../webServices/newsreader.html">Jalview
118 news</a> on startup (not recommended other than for classroom /
125 <div align="center">-nousagestats</div>
127 <div align="left">Turn off google analytics usage tracking</div>
132 <div align="center">-[no]sortbytree</div>
134 <div align="left">Enable or disable automatic sorting of
135 associated view when a new tree is displayed</div>
140 <div align="center">-groovy FILE/URL</div>
142 <div align="left">Execute groovy script in FILE (where
143 FILE may be 'STDIN' to read from the standard input) after all
144 other arguments have been processed</div>
149 <div align="center">-jabaws URL</div>
151 <div align="left">Specify the URL of the preferred JABAWS
157 <div align="center">-fasta FILE</div>
161 <div align="left">Create alignment file FILE in Fasta
166 <td><div align="center">-clustal FILE</div></td>
167 <td><div align="left">Create alignment file FILE in
168 Clustal format.</div></td>
171 <td><div align="center">-msf FILE</div></td>
173 <td><div align="left">Create alignment file FILE in MSF
177 <td><div align="center">-pileup FILE</div></td>
178 <td><div align="left">Create alignment file FILE in
179 Pileup format.</div></td>
182 <td><div align="center">-pir FILE</div></td>
184 <td><div align="left">Create alignment file FILE in PIR
188 <td><div align="center">-pfam FILE</div></td>
189 <td><div align="left">Create alignment file FILE in
190 PFAM format.</div></td>
193 <td><div align="center">-blc FILE</div></td>
194 <td><div align="left">Create alignment file FILE in BLC
198 <td><div align="center">-json FILE</div></td>
199 <td><div align="left">Create alignment file FILE in
200 JSON format.</div></td>
203 <td><div align="center">-jalview FILE</div></td>
205 <td><div align="left">Create alignment file FILE in
206 Jalview format.</div></td>
209 <td><div align="center">-png FILE</div></td>
210 <td><div align="left">Create PNG image FILE from
211 alignment.</div></td>
214 <td><div align="center">-imgMap FILE</div></td>
216 <td><div align="left">Create HTML file FILE with image
217 map of PNG image.</div></td>
220 <td><div align="center">-eps FILE</div></td>
221 <td><div align="left">Create EPS file FILE from
222 alignment.</div></td>
225 <td><div align="center">-svg FILE</div></td>
226 <td><div align="left">Create Scalable Vector Graphics
227 file FILE from alignment.</div></td>
230 <td><div align="center">-biojsMSA FILE</div></td>
231 <td><div align="left">Write an HTML page to display
232 the alignment with the <a href="biojsmsa.html">
233 BioJS MSAviewer MSA</a>
238 <td><div align="center">-jvmmempc=PERCENT</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 PERCENT% of total physical memory detected.
241 This defaults to 90 if total physical memory can be detected.
242 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
247 <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
248 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
249 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
250 gigabytes(g) or if you're lucky enough, terabytes(t).
251 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
252 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.