--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<title>Jalview Command Line Arguments (next generation)</title>
+<body>
+
+ <h1>Jalview Command Line Arguments (version 2.11.3.0 and later)</h1>
+
+ <p>
+ From version 2.11.3.0 Jalview processes a new set of command line arguments
+ which allow more powerful and flexible combinations of arguments, though can
+ also be used for very simple use cases too.
+ </p>
+
+ <p>
+ These new arguments are all accessed with a <code>--doubledash</code> form of
+ command line argument (with the one exception where simply opening one or more
+ files can be performed without any arguments other than the filenames).
+ </p>
+
+ <p>
+ The old command line arguments can still be used (see
+ <a href="clarguments.html">the old page on command line arguments</a>) so
+ existing scripts utilising them should not break.
+ </p>
+
+ <p>
+ However, you cannot mix old and new style arguments, so if you use any
+ <code>-singledash</code> arguments, they will all be interpreted as
+ old style arguments with the new <code>--doubledash</code>
+ arguments being ignored. If you have a script
+ that uses the old arguments without any dashes, and uses the bare-word
+ <code>open</code> then these will also be interpreted as old style arguments.
+ <br/>
+ <strong>Note!</strong> If you use command line arguments without any dashes and
+ <em>don't</em> use the bare-word argument <code>open</code> then all
+ your arguments will be interpreted as alignment files to be opened by the
+ new command line argument process.
+ </p>
+
+ <p>
+ To launch Jalview from the command line, see
+ <a href="commandline.html">running Jalview from the command line</a>.
+ </p>
+
+
+ <h2>Processing command line arguments</h2>
+
+ <p>
+ Jalview no longer necessarily processes arguments sequentially, although
+ in typical use cases you may still want to think of it as doing so.
+ <br/>
+ For more advanced use please see
+ <a href="advancedclarguments.html">Advanced Command Line Arguments</a>.
+ </p>
+
+
+ <h3>Typical Use Cases</h3>
+
+ <h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--newframe</code>)</h4>
+
+ <p>
+ To simply open one or more alignment files in different frames just put the filenames as the first arguments:
+ <pre>
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ You can use shell-expanded wildcards:
+ <pre>
+ jalview this/filename* that/filename* other/filename*
+ </pre>
+ and URLs:
+ <pre>
+ jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <p>
+ (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
+ after the initial filenames.)
+ </p>
+
+ <h5 name="--open"><code>--open</code></h5>
+
+ <p>
+ Use the <code>--open</code> argument to open alignment files each in their own frame.
+ </p>
+
+ <p>
+ The following are equivalent:
+ <pre>
+ jalview --open filename1 filename2 ...
+
+ jalview --open filename*
+
+ jalview --open filename1 --open filename2 --open ...
+
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ Similarly you can open URLs:
+ <pre>
+ jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <h5 name="--append"><code>--append</code></h5>
+
+ <p>
+ To append several alignment files together use:
+ <pre>
+ jalview --open filename1.fa --append filename2.fa filename3.fa
+ </pre>
+ 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:
+ <pre>
+ jalview --append these/filename*.fa --append more/filename*.fa
+
+ jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry
+ </pre>
+ </p>
+
+ <h5 name="--newframe"><code>--newframe</code></h5>
+
+ <p>
+ To append different sets of alignment files in different frames, use <code>--newframe</code> to move on to a new alignment frame:
+ <pre>
+ jalview --append these/filename*.fa --newframe --append other/filename*.fa
+ </pre>
+ </p>
+
+ <p>
+ <code>--open</code> is like using <code>--newframe --append</code> applied to every filename/URL given to <code>--open</code>
+ </p>
+
+
+ <h4 name="">(<code></code>)</h4>
+
+ <p>
+ </p>
+
+ <h5 name=""><code>--</code></h5>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+
+
+ </table>
+
+
+
+
+
+
+
+ <p>
+ Jalview processes arguments on the command line sequentially. If
+ you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
+ <a href="../memory.html">memory settings</a> or any other launch
+ parameters, then include it at the beginning of the command line to
+ ensure they are processed before any remaining arguments.
+ <br>
+ Typical command line execution follows the following pattern:
+ <pre>
+ jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+ </pre>
+
+ <table width="100%" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="27%"><div align="center">-nodisplay</div></td>
+ <td width="73%"><div align="left">Run Jalview without
+ User Interface. (automatically disables questionnaire, version
+ and usage stats checks)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-nowebservicediscovery</div></td>
+ <td><div align="left">Do not query configured servers to
+ discover web services (<em>Since 2.11.2.0</em>)</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-open FILE/URL</div></td>
+ <td><div align="left">Specify the alignment file to
+ open or process by providing additional arguments.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-props FILE/URL</div></td>
+ <td><div align="left">Use the given Jalview properties
+ file instead of users default.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-setprop PROPERTY=value</div></td>
+ <td><div align="left">(JalviewJS ONLY) sets the given
+ property to the given value</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-features FILE/URL</div></td>
+ <td><div align="left">
+ <p>
+ Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features
+ File</a> (Known as Groups file prior to 2.08) description.
+ </p>
+
+ </div></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-colour COLOURSCHEME</div>
+ </td>
+ <td>Set the colourscheme for the alignment. This can be any
+ of the built-in colourschemes, a name of a predefined
+ colourscheme (defined in the Jalview properties file), or an
+ 'inline' colourscheme (see the applet's colour parameter for
+ more information).</td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-annotations FILE/URL</div>
+ </td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW">Annotation
+ File</a> description.
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-no-annotation</div>
+ </td>
+ <td>Do not display annotation below the alignment.
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ <div align="center">-tree FILE/URL</div>
+ <td>
+ <div align="left">Load the given newick format tree file
+ onto the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information
+ about any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <div align="left">Turn off questionnaire check</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">
+ Disable check for <a href="../webServices/newsreader.html">Jalview
+ news</a> on startup (not recommended other than for classroom /
+ demo usage)
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of
+ associated view when a new tree is displayed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE/URL</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where
+ FILE may be 'STDIN' to read from the standard input) after all
+ other arguments have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-jabaws URL</div>
+ <td>
+ <div align="left">Specify the URL of the preferred JABAWS
+ server</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>
+
+ <td>
+ <div align="left">Create alignment file FILE in Fasta
+ format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in MSF
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in PIR
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ JSON format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
+
+ <td><div align="left">Create alignment file FILE in
+ Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
+
+ <td><div align="left">Create HTML file FILE with image
+ map of PNG image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-svg FILE</div></td>
+ <td><div align="left">Create Scalable Vector Graphics
+ file FILE from alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-biojsMSA FILE</div></td>
+ <td><div align="left">Write an HTML page to display
+ the alignment with the <a href="biojsmsa.html">
+ BioJS MSAviewer MSA</a>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmempc=PERCENT</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+ This defaults to 90 if total physical memory can be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
+ <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+ gigabytes(g) or if you're lucky enough, terabytes(t).
+ This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </div>
+ </td>
+ </tr>
+ </table>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff