3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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22 <title>Jalview Command Line Arguments (next generation)</title>
25 <h1>Jalview Command Line Arguments (version 2.11.3.0 and later)</h1>
28 From version 2.11.3.0 Jalview processes a new set of command line arguments
29 which allow more powerful and flexible combinations of arguments, though can
30 also be used for very simple use cases too.
34 These new arguments are all accessed with a <code>--doubledash</code> form of
35 command line argument (with the one exception where simply opening one or more
36 files can be performed without any arguments other than the filenames).
40 The old command line arguments can still be used (see
41 <a href="clarguments.html">the old page on command line arguments</a>) so
42 existing scripts utilising them should not break.
46 However, you cannot mix old and new style arguments, so if you use any
47 <code>-singledash</code> arguments, they will all be interpreted as
48 old style arguments with the new <code>--doubledash</code>
49 arguments being ignored. If you have a script
50 that uses the old arguments without any dashes, and uses the bare-word
51 <code>open</code> then these will also be interpreted as old style arguments.
53 <strong>Note!</strong> If you use command line arguments without any dashes and
54 <em>don't</em> use the bare-word argument <code>open</code> then all
55 your arguments will be interpreted as alignment files to be opened by the
56 new command line argument process.
60 To launch Jalview from the command line, see
61 <a href="commandline.html">running Jalview from the command line</a>.
65 <h2>Processing command line arguments</h2>
68 Jalview no longer necessarily processes arguments sequentially, although
69 in typical use cases you may still want to think of it as doing so.
71 For more advanced use please see
72 <a href="advancedclarguments.html">Advanced Command Line Arguments</a>.
76 <h3>Typical Use Cases</h3>
78 <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--newframe</code>)</h4>
81 To simply open one or more alignment files in different frames just put the filenames as the first arguments:
83 jalview filename1 filename2 ...
88 You can use shell-expanded wildcards:
90 jalview this/filename* that/filename* other/filename*
94 jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
99 (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
100 after the initial filenames.)
103 <h5 name="--open"><code>--open</code></h5>
106 Use the <code>--open</code> argument to open alignment files each in their own frame.
110 The following are equivalent:
112 jalview --open filename1 filename2 ...
114 jalview --open filename*
116 jalview --open filename1 --open filename2 --open ...
118 jalview filename1 filename2 ...
123 Similarly you can open URLs:
125 jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
129 <h5 name="--append"><code>--append</code></h5>
132 To append several alignment files together use:
134 jalview --open filename1.fa --append filename2.fa filename3.fa
136 or, if you haven't previously used <code>--open</code> then you can use --append to open one new frame and keep appending each set of alignments:
138 jalview --append these/filename*.fa --append more/filename*.fa
140 jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
144 <h5 name="--newframe"><code>--newframe</code></h5>
147 To append different sets of alignment files in different frames, use <code>--newframe</code> to move on to a new alignment frame:
149 jalview --append these/filename*.fa --newframe --append other/filename*.fa
154 <code>--open</code> is like using <code>--newframe --append</code> applied to every filename/URL given to <code>--open</code>
158 <h4 name="">(<code></code>)</h4>
163 <h5 name=""><code>--</code></h5>
181 Jalview processes arguments on the command line sequentially. If
182 you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
183 <a href="../memory.html">memory settings</a> or any other launch
184 parameters, then include it at the beginning of the command line to
185 ensure they are processed before any remaining arguments.
187 Typical command line execution follows the following pattern:
189 jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
192 <table width="100%" border="1" cellspacing="0" cellpadding="0">
194 <td width="27%"><div align="center">-nodisplay</div></td>
195 <td width="73%"><div align="left">Run Jalview without
196 User Interface. (automatically disables questionnaire, version
197 and usage stats checks)</div></td>
200 <td><div align="center">-nowebservicediscovery</div></td>
201 <td><div align="left">Do not query configured servers to
202 discover web services (<em>Since 2.11.2.0</em>)</div></td>
205 <td><div align="center">-open FILE/URL</div></td>
206 <td><div align="left">Specify the alignment file to
207 open or process by providing additional arguments.</div></td>
210 <td><div align="center">-props FILE/URL</div></td>
211 <td><div align="left">Use the given Jalview properties
212 file instead of users default.</div></td>
215 <td><div align="center">-setprop PROPERTY=value</div></td>
216 <td><div align="left">(JalviewJS ONLY) sets the given
217 property to the given value</div></td>
220 <td><div align="center">-features FILE/URL</div></td>
221 <td><div align="left">
223 Use the given file to add sequence features to an alignment.
224 See <a href="featuresFormat.html" target="NEW">Features
225 File</a> (Known as Groups file prior to 2.08) description.
232 <div align="center">-colour COLOURSCHEME</div>
234 <td>Set the colourscheme for the alignment. This can be any
235 of the built-in colourschemes, a name of a predefined
236 colourscheme (defined in the Jalview properties file), or an
237 'inline' colourscheme (see the applet's colour parameter for
238 more information).</td>
242 <div align="center">-annotations FILE/URL</div>
244 <td>Add precalculated annotations to the alignment. See <a
245 href="annotationsFormat.html" target="NEW">Annotation
246 File</a> description.
251 <div align="center">-no-annotation</div>
253 <td>Do not display annotation below the alignment.
259 <div align="center">-tree FILE/URL</div>
261 <div align="left">Load the given newick format tree file
262 onto the alignment</div>
267 <div align="center">-questionnaire URL</div>
269 <div align="left">Queries the given URL for information
270 about any Jalview user questionnaires</div>
275 <div align="center">-noquestionnaire</div>
277 <div align="left">Turn off questionnaire check</div>
282 <div align="center">-nonews</div>
285 Disable check for <a href="../webServices/newsreader.html">Jalview
286 news</a> on startup (not recommended other than for classroom /
293 <div align="center">-nousagestats</div>
295 <div align="left">Turn off google analytics usage tracking</div>
300 <div align="center">-[no]sortbytree</div>
302 <div align="left">Enable or disable automatic sorting of
303 associated view when a new tree is displayed</div>
308 <div align="center">-groovy FILE/URL</div>
310 <div align="left">Execute groovy script in FILE (where
311 FILE may be 'STDIN' to read from the standard input) after all
312 other arguments have been processed</div>
317 <div align="center">-jabaws URL</div>
319 <div align="left">Specify the URL of the preferred JABAWS
325 <div align="center">-fasta FILE</div>
329 <div align="left">Create alignment file FILE in Fasta
334 <td><div align="center">-clustal FILE</div></td>
335 <td><div align="left">Create alignment file FILE in
336 Clustal format.</div></td>
339 <td><div align="center">-msf FILE</div></td>
341 <td><div align="left">Create alignment file FILE in MSF
345 <td><div align="center">-pileup FILE</div></td>
346 <td><div align="left">Create alignment file FILE in
347 Pileup format.</div></td>
350 <td><div align="center">-pir FILE</div></td>
352 <td><div align="left">Create alignment file FILE in PIR
356 <td><div align="center">-pfam FILE</div></td>
357 <td><div align="left">Create alignment file FILE in
358 PFAM format.</div></td>
361 <td><div align="center">-blc FILE</div></td>
362 <td><div align="left">Create alignment file FILE in BLC
366 <td><div align="center">-json FILE</div></td>
367 <td><div align="left">Create alignment file FILE in
368 JSON format.</div></td>
371 <td><div align="center">-jalview FILE</div></td>
373 <td><div align="left">Create alignment file FILE in
374 Jalview format.</div></td>
377 <td><div align="center">-png FILE</div></td>
378 <td><div align="left">Create PNG image FILE from
379 alignment.</div></td>
382 <td><div align="center">-imgMap FILE</div></td>
384 <td><div align="left">Create HTML file FILE with image
385 map of PNG image.</div></td>
388 <td><div align="center">-eps FILE</div></td>
389 <td><div align="left">Create EPS file FILE from
390 alignment.</div></td>
393 <td><div align="center">-svg FILE</div></td>
394 <td><div align="left">Create Scalable Vector Graphics
395 file FILE from alignment.</div></td>
398 <td><div align="center">-biojsMSA FILE</div></td>
399 <td><div align="left">Write an HTML page to display
400 the alignment with the <a href="biojsmsa.html">
401 BioJS MSAviewer MSA</a>
406 <td><div align="center">-jvmmempc=PERCENT</div></td>
407 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
408 Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
409 This defaults to 90 if total physical memory can be detected.
410 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
415 <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
416 <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
417 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
418 gigabytes(g) or if you're lucky enough, terabytes(t).
419 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
420 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.