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<h2>Shasta commands</h2>
<p>
Shasta is most commonly used to run an assembly.
However, it offers additional utility functions
via command line option
<a href="CommandLineOptions.html#command"><code>--command</code></a>.
Following <code>--command</code>, you specify a command name
which can be one of the following:
<ul>
<li><code>assemble</code>
<li><code>cleanupBinaryData</code>
<li><code>createBashCompletionScript</code>
<li><code>explore</code>
<li><code>listCommands</code>
<li><code>listConfiguration</code>
<li><code>listConfigurations</code>
<li><code>saveBinaryData</code>
</ul>
You can also use the following to get an up to date list
of valid Shasta commands:
<br>
<code>
shasta --command listCommands
</code>
<br>
The default command is <code>assemble</code>, so you don't need to use the
<code>--command</code> option to run an assembly.
<p>
The rest of this page provides a brief description of the functionality
offered by each of these commands.
<h3 id=assemble>Command <code>assemble</code></h3>
<p>
This is the default command and is used to run an assembly.
See <a href="Running.html">here</a> for more information.
<h3 id=cleanupBinaryData>Command <code>cleanupBinaryData</code></h3>
<p>
This command is used to unmount the filesystem in memory used to
hold Shasta binary data, mounted at the <code>Data</code>
directory under the assembly directory.
It frees the memory (in 4 Kb or 2 MB pages
depending on the setting of <code>--memoryBacking</code>)
used to store data in the filesystem.
<p>
It also removes the <code>Data</code> directory.
If a <code>DataOnDisk</code> directory exists,
it creates a symbolic link named <code>Data</code>.
This makes it possible to use the Shasta http server functionality
and Python API even after the binary data are
no longer in memory, as long as they were saved
on disk using <a href="#saveBinaryData"><code>--command saveBinaryData</code></a>.
<p>
This command may require root privilege via <code>sudo</code>,
depending on the setting of
<code>--memoryBacking</code>.
See <a href="Running.html">here</a> for more information.
<h3>Command <code>createBashCompletionScript</code></h3>
<p>
Running this command creates a Bash completion script
that completes Shasta commands to facilitate typing.
The script is named <code>shastaCompletion.sh</code>
and can be invoked from a Bash shell as follows:
<code>
source shastaCompletion.sh
</code>
<p>
See <a href="CommandLineOptions.html#bashCompletion">here</a> for more information.
<h3>Command <code>explore</code></h3>
<p>
This command starts Shasta in a mode that behaves as an
http server. You can use a browser to connect to it
and visualize detailed information about your assembly, and this requires the binary data for the assembly to be available.
See <a href="InspectingResults.html">here</a> for more details.
<h3>Command <code>listCommands</code></h3>
<p>
This command prints an updated list of all
valid commands known to the Shasta executable
being invoked.
<h3>Command <code>listConfiguration</code></h3>
<p>
A configuration is a built-in set of Shasta command line options
that can be selected by name.
To print details of a specific configuration, use:
<code>
shasta --command listConfiguration --config Name
</code>
For example,
<code>
shasta --command listConfiguration --config Nanopore-Sep2020
</code>
To see a list of available configuration names, use
<code>
shasta --command listConfigurations
</code>
<p>
You can also create a configuration with
command line options that you select
and store it in a file.
See <a href="Configurations.html#ConfigFile">here</a>
for more information.
<h3>Command <code>listConfigurations</code></h3>
<p>
A configuration is a built-in set of Shasta command line options
that can be selected by name.
This command prints a list of the available configurations.
See <a href="Configurations.html#ConfigFile">here</a>
for more information.
<h3 id=saveBinaryData>Command <code>saveBinaryData</code></h3>
<p>
This command is used to save Shasta binary data.
Shasta stores binary data in directory <code>Data</code> in the assembly directory.
This command makes a copy on disk in <code>Data</code>.
You will usually want to run
<code>--command cleanupBinaryData</code>
after this command completes.
<p>
This command may require root privilege via <code>sudo</code>,
depending on the setting of
<code>--memoryBacking</code>.
See <a href="Running.html">here</a> for more information.
<p>
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