Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / help / help / html / memory.html

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index ec57530..17dc557 100755 (executable)
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -74,6 +74,11 @@
       with a different percentage of physical memory available is to
       adjust your user preferences via the <a
       ref="preferences.html#startup">Startup Preferences</a> panel.</li>
+    <li>
+      <em><code>jalview</code> command line launch</em>
+      <br/>
+      When starting Jalview from a <a href="features/commandline.html">command line launch</a> you can use the memory setting arguments <a href="features/clarguments.html#jvmmemmax"><code>--jvmmemmax=MAXMEMORY</code></a> and <a href="features/clarguments.html#jvmmempc"><code>--jvmmempc=PERCENT</code></a>.  <code>MAXMEMORY</code> should be an integer optionally followed by one of <code>k</code>, <code>m</code>, <code>g</code>, <code>t</code>.  <code>PERCENT</code> should be an integer between 1 and 100.
+    </li>
     <li><em><font size="3">JVL file</font></em> <br />Another way
       to adjust launch settings is with a text file with extension <em>.jvl</em>
       and a single line to specify the percentage of memory you wish
@@ -90,12 +95,12 @@
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre>
       Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. <pre>
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl --open https://www.jalview.org/examples/jpred_msa.fasta --annotations https://www.jalview.org/examples/jpred_msa.seq.concise --colour Clustal</pre>
       You can use command line arguments to control memory settings in
       Windows and macOS too: <br /> In Windows you must use, e.g. <pre>
-      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre>
+      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl --open %HOMEPATH%\myalignment.fa</pre>
       In macOS you can use the macOS <em>open</em> command like this: <pre>
-      open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put
+      open /Applications/Jalview.app --args ~/mymemorysetting.jvl --open ~/myalignment.fa</pre><em>(put
         all the Jalview arguments <em>after</em> the --args parameter)
     </em><br />
     <br /></li>
@@ -107,9 +112,9 @@
     </li>
     <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
       If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
-      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
-      and <em>-jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
-      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
+      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>--jvmmempc=PERCENT</em>
+      and <em>--jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
+      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar --jvmmempc=50 --jvmmemmax=20g</pre>
       (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
       <br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
       <br/><br/>