Shasta commands
Shasta is most commonly used to run an assembly.
However, it offers additional utility functions
via command line option
--command.
Following --command, you specify a command name
which can be one of the following:
assemblecleanupBinaryDatacreateBashCompletionScriptexplorelistCommandslistConfigurationlistConfigurationssaveBinaryData
shasta --command listCommands
The default command is
assemble, so you don't need to use the
--command option to run an assembly.
The rest of this page provides a brief description of the functionality offered by each of these commands.
Command assemble
This is the default command and is used to run an assembly. See here for more information.
Command cleanupBinaryData
This command is used to unmount the filesystem in memory used to
hold Shasta binary data, mounted at the Data
directory under the assembly directory.
It frees the memory (in 4 Kb or 2 MB pages
depending on the setting of --memoryBacking)
used to store data in the filesystem.
It also removes the Data directory.
If a DataOnDisk directory exists,
it creates a symbolic link named Data.
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 --command saveBinaryData.
This command may require root privilege via sudo,
depending on the setting of
--memoryBacking.
See here for more information.
Command createBashCompletionScript
Running this command creates a Bash completion script
that completes Shasta commands to facilitate typing.
The script is named shastaCompletion.sh
and can be invoked from a Bash shell as follows:
source shastaCompletion.sh
See here for more information.
Command explore
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 here for more details.
Command listCommands
This command prints an updated list of all valid commands known to the Shasta executable being invoked.
Command listConfiguration
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:
shasta --command listConfiguration --config Name
For example,
shasta --command listConfiguration --config Nanopore-Sep2020
To see a list of available configuration names, use
shasta --command listConfigurations
You can also create a configuration with command line options that you select and store it in a file. See here for more information.
Command listConfigurations
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 here for more information.
Command saveBinaryData
This command is used to save Shasta binary data.
Shasta stores binary data in directory Data in the assembly directory.
This command makes a copy on disk in Data.
You will usually want to run
--command cleanupBinaryData
after this command completes.
This command may require root privilege via sudo,
depending on the setting of
--memoryBacking.
See here for more information.