Modifier and Type | Class and Description |
---|---|
class |
DockerBuilder
Docker container builder.
|
class |
LocalBuilder
Local command builder.
|
class |
SingularityBuilder
Singularity container builder.
|
Modifier and Type | Method and Description |
---|---|
CommandBuilder |
CommandBuilder.add(Iterable<String> arguments)
Add one or more arguments to the list of command arguments for this command builder.
|
CommandBuilder |
CommandBuilder.add(String... arguments)
Add one or more arguments to the list of command arguments for this command builder.
|
CommandBuilder |
CommandBuilder.addArgument(String argument)
Add an argument to the list of command arguments for this command builder.
|
CommandBuilder |
CommandBuilder.addArguments(Iterable<String> arguments)
Add one or more arguments to the list of command arguments for this command builder.
|
CommandBuilder |
CommandBuilder.addArguments(String... arguments)
Add one or more arguments to the list of command arguments for this command builder.
|
CommandBuilder |
CommandBuilder.addEnvironment(Map<String,String> environment)
Add environment variables to the map of environment variables for this command builder.
|
CommandBuilder |
CommandBuilder.addEnvironment(String variable,
String value)
Add an environment variable to the map of environment variables for this command builder.
|
CommandBuilder |
CommandBuilder.addFile(String file)
Add a file to the list of files to make available locally for this command builder.
|
CommandBuilder |
CommandBuilder.addFiles(Iterable<String> files)
Add files to the list of files to make available locally for this command builder.
|
CommandBuilder |
CommandBuilder.addFiles(String... files)
Add zero or more files to the list of files to make available locally for this command builder.
|
CommandBuilder |
CommandBuilder.addMount(String mount)
Add the specified mount point to the map of mount points for this command builder.
|
CommandBuilder |
CommandBuilder.addMount(String source,
String target)
Add the specified mount point to the map of mount points for this command builder.
|
CommandBuilder |
CommandBuilder.addMounts(Map<String,String> mounts)
Add the specified mount points to the map of mount points for this command builder.
|
static CommandBuilder |
CommandBuilders.create(boolean useDocker,
boolean useSingularity)
Create a new Cannoli pipe command builder.
|
CommandBuilder |
CommandBuilder.reset()
Reset this command builder.
|
CommandBuilder |
CommandBuilder.setExecutable(String executable)
Set the executable for this command builder.
|
CommandBuilder |
CommandBuilder.setFlankSize(Integer flankSize)
Set the number of bases to flank each command invocation by for this builder.
|
CommandBuilder |
CommandBuilder.setImage(String image)
Set the image for this command builder.
|
CommandBuilder |
CommandBuilder.setSudo(boolean sudo)
Set to true to run via sudo for this command builder.
|
CommandBuilder |
CommandBuilder.setTimeout(Long timeout)
Set how long to let a single partition run for, in seconds, for this builder.
|
CommandBuilder |
CommandBuilder.setTimeout(long duration,
TimeUnit timeUnit)
Set how long to let a single partition run for, in the specified time unit, for this builder.
|
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