- Difficulty level: easy
- Time need to lean: 10 minutes or less
- Key points:
- This tutorial lists the command line options of
soscommand
- This tutorial lists the command line options of
Command sos accepts a number of subcommands (similar to svn, git etc). Its syntax follows
sos subcommand [subcommand-options]
You can use command
In [2]:
usage: sos [-h] [--version]
{install,run,dryrun,status,execute,kill,purge,config,convert,remove}
...
A workflow system for the execution of commands and scripts in different
languages.
options:
-h, --help show this help message and exit
--version show program's version number and exit
subcommands:
{install,run,dryrun,status,execute,kill,purge,config,convert,remove}
run Execute default or specified workflow in script
dryrun Execute workflow in dryrun mode
status Check the status of specified tasks
remote Listing and testing remote configurations
execute Execute a packages task
kill Stop the execution of running task
purge Remove local or remote tasks or workflows
config Read and write sos configuration files
convert Convert between .sos, .ipynb and other formats
remove Remove specified files and/or their signatures
Use 'sos cmd -h' for details about each subcommand. Please contact Bo Peng
(bpeng at mdanderson.org) if you have any question.
to get a list of subcommands with brief descriptions and
sos subcommand -h
to get detailed description of a particular subcommand.
Command sos-runner is a shortcut for sos run so
% sos-runner script
is equivalent to
% sos run script
This allows a SoS script to be executed directly if it is executable with shebang line
#!/usr/bin/env sos-runner
In [2]:
usage: sos run [-h] [-j [WORKERS [WORKERS ...]]] [-J EXTERNAL_JOBS]
[-c CONFIG_FILE] [-t FILE [FILE ...]] [-q QUEUE [QUEUE ...]]
[-r HOST [HOST ...]] [-n] [-s SIGMODE] [-T] [-e ERRORMODE]
[-d [DAG]] [-p [REPORT]] [-v {0,1,2,3,4}]
SCRIPT [WORKFLOW]
Execute default or specified workflow defined in script
positional arguments:
SCRIPT A SoS script that defines one or more workflows, in
format .sos or .ipynb. The script can be a filename or
a URL from which the content of a SoS will be read. If
a valid file cannot be located or downloaded, SoS will
search for the script, with specified name, and with
added extension .sos and .ipynb, in a search path
specified by variable `sos_path` defined in the global
SoS configuration file (~/.sos/config.yml).
WORKFLOW Name of the workflow to execute. This option can be
ignored if the script defines a default workflow (with
no name or with name `default`) or defines only a
single workflow. A subworkflow or a combined workflow
can also be specified, where a subworkflow executes a
subset of workflow (`name_steps` where `steps` can be
`n` (a step `n`), `:n` (up to step `n`), `n:m` (from
step `n` to `m`), and `n:` (from step `n`)), and a
combined workflow executes to multiple (sub)workflows
combined by `+` (e.g. `A_0+B+C`).
optional arguments:
-h, --help show this help message and exit
-j [WORKERS [WORKERS ...]]
Hosts and number of worker processes in each host for
the execution of workflow, default to local host with
half the number of CPUs, or 8, whichever is smaller.
The complete format of this option is "-j host1:n1
host2:n2 host3:n3 ..." which are name, ip or alias
(defined in sos configurations) of local or remote
hosts, and number of processes on each host. If left
unspecified, host will be assumed to be the host on
which the master SoS process is started, and n is half
of the number of CPUs on the host, or 8 if there are
more than 16 CPUs. If there are a large number of
hosts, the parameters are usually speified through a
hostfile with values in each line, and be specified in
the format of "-j @hostfile". On a supported cluster
system where environmental variables such as
"PBS_HOSTFILE" are specified, SoS will ignore this
parameter and read worker information from the host
file.
-J EXTERNAL_JOBS Maximum number of externally running tasks. This
option overrides option "max_running_jobs" of a task
queue (option -q) so that you can, for example, submit
one job at a time (with -J 1) to test the task queue.
-c CONFIG_FILE A configuration file in the format of YAML/JSON. The
content of the configuration file will be available as
a dictionary CONF in the SoS script being executed.
-t FILE [FILE ...] One of more files or names of named outputs that will
be the target of execution. If specified, SoS will
execute only part of a workflow or multiple workflows
or auxiliary steps to generate specified targets.
-q QUEUE [QUEUE ...] host (server) or job queues to execute all tasks in
the workflow. The queue can be name, IP, or an alias
defined in SoS configuration files. A host is assumed
to be a remote host with process type unless other
queue types and related information are defined in the
host file. If left unspecified, tasks are executed as
part of the regular step processes unless task-
specific queues are specified. Optional KEY=VALUE
pairs could be specified after queue name and be used
to expand task or workflow templates. These options
will override task options if the options with the
same name is defined.
-r HOST [HOST ...] Execute the workflow in specified remote (or local)
host, which should be defined under key "hosts" of sos
configurations (preferrably in ~/.sos/hosts.yml). This
option basically copies the script to specified host
and executes it with the "workflow_engine" of the
host, which is by default a "process" engine that
execute the workflow with an opotional
"workflow_template" defined for the host. The
"workflow_template" is expanded with "filename" being
the path of script, "script" being the content of the
script (extracted from notebook if "filename" is a
notebook), "command" being the command line to execute
the script, as specified from the command line but
with options "-r", and "-c" removed, "KEY" being
"VALUE" from "KEY=VALUE" pairs defined after the
"host" name. For example, "-r cluster cores=4 mem=5G"
would expand variables "cores" and "mem" in the
template with values "4" and "5G".
Run mode options:
Control how sos scirpt is executed.
-n Execute a workflow in dryrun mode. Please check
command sos dryrun for details of the dryrun mode.
-s SIGMODE How runtime signature would be handled, which can be
"default" (save and use signature, default mode in
batch mode), "ignore" (ignore runtime signature,
default mode in interactive mode), "force" (ignore
existing signature and overwrite them while executing
the workflow), "build" (build new or overwrite
existing signature from existing environment and
output files), and "assert" for validating existing
files against their signatures. "skip" and
"distributed" are two experimental modes with "skip"
for bypassing substep as long as step output exists
and later than input files and "distributed" for
sending tasks to subworkers for signature validation.
Please refer to online documentation for details about
the use of runtime signatures.
-T Trace existing targets and re-execute the steps that
generate them to make sure that the targets are
current.
-e ERRORMODE How to handle failures from steps and substeps. By
default, after an error happens and stops the
execution of a step, SoS will exit after it executes
the rest of the DAG until all unaffected steps are
executede. You can specify "-e abort" if you would
like SoS to stop as soon as any error is detected, or
"-e ignore" to ignore the error and continue to
execute the workflow as best as it can.
Output options:
Output of workflow
-d [DAG] Output Direct Acyclic Graph (DAGs) in graphiviz .dot
format. Because DAG and status of nodes will change
during the execution of workflow, multiple DAGs will
be written to the specified file with names
{workflow}_1, {workflow}_2 etc. The dot file would be
named {script_name}_{timestamp}.dot unless a separate
filename is specified.
-p [REPORT] Output a report that summarizes the execution of the
workflow after the completion of the execution. This
includes command line, steps executed, tasks executed,
CPU/memory of tasks, and DAG if option -d is also
specified. The report will by be named
{script_name}_{timestamp}.html unless a separate
filename is specified.
-v {0,1,2,3,4} Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
Arbitrary parameters defined by the [parameters] step of the script, and
[parameters] steps of other scripts if nested workflows are defined in other
SoS files (option `source`). The name, default and type of the parameters are
specified in the script. Single value parameters should be passed using option
`--name value` and multi-value parameters should be passed using option
`--name value1 value2`.
Please refer to section SoS Syntax of the documentation for details about this command.
In [3]:
usage: sos dryrun [-h] [-c CONFIG_FILE] [-t FILES [FILES ...]] [-q QUEUE] [-T]
[-d [DAG]] [-p [REPORT]] [-v {0,1,2,3,4}]
SCRIPT [WORKFLOW]
Execute workflow in dryrun mode. This mode is identical to run mode except
that 1). Actions might behavior differently. In particular, script-running
steps would print instead of execute script. 2). Steps will generate empty
output files if specified output do not exist after execution. 3). Signature
mode is set to ignore. 4). Option -q is ignored so all tasks are executed
locally. 5). Tasks are generated but not executed.
positional arguments:
SCRIPT A SoS script that defines one or more workflows, in
format .sos or .ipynb. The script can be a filename or
a URL from which the content of a SoS will be read. If
a valid file cannot be located or downloaded, SoS will
search for the script, with specified name, and with
added extension .sos and .ipynb, in a search path
specified by variable `sos_path` defined in the global
SoS configuration file (~/.sos/config.yml).
WORKFLOW Name of the workflow to execute. This option can be
ignored if the script defines a default workflow (with
no name or with name `default`) or defines only a
single workflow. A subworkflow or a combined workflow
can also be specified, where a subworkflow executes a
subset of workflow (`name_steps` where `steps` can be
`n` (a step `n`), `:n` (up to step `n`), `n:m` (from
step `n` to `m`), and `n:` (from step `n`)), and a
combined workflow executes to multiple (sub)workflows
combined by `+` (e.g. `A_0+B+C`).
optional arguments:
-h, --help show this help message and exit
-c CONFIG_FILE A configuration file in the format of YAML/JSON. The
content of the configuration file will be available as
a dictionary CONF in the SoS script being executed.
-t FILES [FILES ...] One of more files or alias of other targets that will
be the target of execution. If specified, SoS will
execute only part of a workflow or multiple workflows
or auxiliary steps to generate specified targets.
-q QUEUE host (server) or job queues to execute all tasks in
the workflow. The queue can be defined in global or
local sos configuration file, or a file specified by
option --config. A host is assumed to be a remote
machine with process type if no configuration is
found.
Run mode options:
Control how sos scirpt is executed.
-T Trace existing targets and re-execute the steps that
generate them to make sure that the targets are
current.
Output options:
Output of workflow
-d [DAG] Output Direct Acyclic Graph (DAGs) in graphiviz .dot
format. An exntesion of ".dot" would be added
automatically. Because DAG could change during the
execution of workflow, multiple DAGs could be outputed
with names $FILE_1.dot, $FILE_2.dot. If this option is
specified without a name, the DAG would be wrritten to
the standard output.
-p [REPORT] Output a report that summarizes the execution of the
workflow after the completion of the execution. This
includes command line, steps executed, tasks executed,
CPU/memory of tasks, and DAG if option -d is also
specified. The report will by be named
{script_name}_{timestamp}.html unless a separate
filename is specified.
-v {0,1,2,3,4} Output error (0), warning (1), info (2), debug (3) and
trace (4) information to standard output (default to
2).
Arbitrary parameters defined by the [parameters] step of the script, and
[parameters] steps of other scripts if nested workflows are defined in other
SoS files (option `source`). The name, default and type of the parameters are
specified in the script. Single value parameters should be passed using option
`--name value` and multi-value parameters should be passed using option
`--name value1 value2`.
Please refer to the tutorial on SoS Workflow for details about this command.
In [4]:
usage: sos remote [-h] [-c CONFIG] [-p PASSWORD] [--files [FILES [FILES ...]]]
[--cmd ...] [-v {0,1,2,3,4}]
{list,status,setup,test,login,push,pull,run}
[hosts [hosts ...]]
Listing and testing remote configurations
positional arguments:
{list,status,setup,test,login,push,pull,run}
List (list), check status of tasks (status), setup
public-key authentication (setup), test configuration
(test), login (login), push files to one or more
remote hosts (push), pull files from a remote host, or
execute command (run) on one or all or specified
remote hosts
hosts Hosts to be checked or tested. All hosts defined in
SoS configurations will be included if unspecified. As
a special case for "sos remote setup", an address is
acceptable even if it is defined in configuration
file.
optional arguments:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
A configuration file with host definitions, in case
the definitions are not defined in global sos
config.yml files.
-p PASSWORD, --password PASSWORD
Password used to copy public key to remote hosts. You
will be prompted for a password if a password is
needed and is not passed from command line. The same
password will be used for all specified hosts so you
will need to use separate setup commands for hosts
with different passwords.
--files [FILES [FILES ...]]
files or directories to be push or pulled for action
"push" or "pull"
--cmd ... commands to be executed by action "run" or tested by
action "test". This option takes all remaining options
of part of command and must be the last option of the
sos remote command.
-v {0,1,2,3,4}, --verbosity {0,1,2,3,4}
Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
In [5]:
usage: sos execute [-h] [-s SIGMODE] [-v {0,1,2,3,4}] [-e EXECUTOR]
[-m RUN_MODE] [-q QUEUE] [-c CONFIG] [-w]
tasks [tasks ...]
Execute a packages task
positional arguments:
tasks IDs of the task.
optional arguments:
-h, --help show this help message and exit
-s SIGMODE How runtime signature would be handled, which can be
"default" (save and use signature, default mode in
batch mode), "force" (ignore existing signature and
overwrite them while executing the workflow), "build"
(build new or overwrite existing signature from
existing environment and output files), and "assert"
for validating existing files against their
signatures. "skip" and "distributed" are two
experimental modes with "skip" for bypassing substep
as long as step output exists and later than input
files and "distributed" for sending tasks to
subworkers for signature validation. Tasks will always
save sigatures. For compatibility reasons, "ignore"
mode is accepted but is treated the same as "default".
Please refer to online documentation for details about
the use of runtime signatures.
-v {0,1,2,3,4} Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
-e EXECUTOR, --executor EXECUTOR
Executor used to execute the task, which should be an
entry point under section sos_taskexecutors that
points to a class with at least a execute member
function.
-m RUN_MODE, --mode RUN_MODE
Run mode of the task, default to 'run', but can be
'dryrun' (the same as --dryrun) or 'interactive",
which suppress status update.
-q QUEUE, --queue QUEUE
Check the status of job on specified tasks queue or
remote host if the tasks . The queue can be defined in
global or local sos configuration file, or a file
specified by option --config. A host is assumed to be
a remote machine with process type if no configuration
is found.
-c CONFIG, --config CONFIG
A configuration file with host definitions, in case
the definitions are not defined in global sos
config.yml files.
-w, --wait Wait for the completion of the task, and retrieve job
results if needed after the completion of the task.
This option is only valid with the specification of
the -q option.
In [6]:
usage: sos status [-h] [-q QUEUE] [-c CONFIG] [-v {0,1,2,3,4}]
[-t [TAGS [TAGS ...]]] [-s [STATUS [STATUS ...]]]
[--age AGE] [--html]
[tasks [tasks ...]]
Check the status of specified tasks
positional arguments:
tasks ID of the task. All tasks that are releted to the
workflow executed under the current directory will be
checked if unspecified. There is no need to specify
compelete task IDs because SoS will match specified
name with tasks starting with these names.
optional arguments:
-h, --help show this help message and exit
-q QUEUE, --queue QUEUE
Check the status of job on specified tasks queue or
remote host if the tasks . The queue can be defined in
global or local sos configuration file, or a file
specified by option --config. A host is assumed to be
a remote machine with process type if no configuration
is found.
-c CONFIG, --config CONFIG
A configuration file with host definitions, in case
the definitions are not defined in global sos
config.yml files.
-v {0,1,2,3,4} Output error (0), warning (1), info (2), debug (3) and
trace (4) information to standard output (default to
2).
-t [TAGS [TAGS ...]], --tags [TAGS [TAGS ...]]
Only list tasks with one of the specified tags.
-s [STATUS [STATUS ...]], --status [STATUS [STATUS ...]]
Display tasks with one of the specified status.
--age AGE Limit to tasks that are created more than (default) or
within specified age. Value of this parameter can be
in units s (second), m (minute), h (hour), or d (day,
default), or in the foramt of HH:MM:SS, with optional
prefix + for older (default) and - for newer than
specified age.
--html Output results in HTML format. This option will
override option verbosity and output detailed status
information in HTML tables and figures.
In [7]:
usage: sos kill [-h] [-a] [-q QUEUE] [-t [TAGS [TAGS ...]]] [-c CONFIG]
[-v {0,1,2,3,4}]
[tasks [tasks ...]]
Stop the execution of running task
positional arguments:
tasks IDs of the tasks that will be killed. There is no need
to specify compelete task IDs because SoS will match
specified name with tasks starting with these names.
optional arguments:
-h, --help show this help message and exit
-a, --all Kill all tasks in local or specified remote task queue
-q QUEUE, --queue QUEUE
Kill jobs on specified tasks queue or remote host if
the tasks . The queue can be defined in global or
local sos configuration file, or a file specified by
option --config. A host is assumed to be a remote
machine with process type if no configuration is
found.
-t [TAGS [TAGS ...]], --tags [TAGS [TAGS ...]]
Only kill tasks with one of the specified tags.
-c CONFIG, --config CONFIG
A configuration file with host definitions, in case
the definitions are not defined in global sos
config.yml files.
-v {0,1,2,3,4}, --verbosity {0,1,2,3,4}
Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
In [8]:
usage: sos purge [-h] [-a | --age AGE | -s STATUS [STATUS ...] | -t
[TAGS [TAGS ...]]] [-q QUEUE] [-c CONFIG] [-v {0,1,2,3,4}]
[tasks [tasks ...]]
Remove local or remote tasks
positional arguments:
tasks ID of the tasks to be removed. There is no need to
specify compelete task IDs because SoS will match
specified name with tasks starting with these names.
If no task ID is specified, all tasks related to
specified workflows (option -w) will be removed.
optional arguments:
-h, --help show this help message and exit
-a, --all Clear all task information on local or specified
remote task queue, including tasks created by other
workflows.
--age AGE Remova all tasks that are created more than (default)
or within specified age. Value of this parameter can
be in units s (second), m (minute), h (hour), or d
(day, default), or in the foramt of HH:MM:SS, with
optional prefix + for older (default) and - for newer
than specified age.
-s STATUS [STATUS ...], --status STATUS [STATUS ...]
Remove all tasks with specified status, which can be
pending, submitted, running, completed, failed, and
aborted. One of more status can be specified.
-t [TAGS [TAGS ...]], --tags [TAGS [TAGS ...]]
Remove all tasks that matches one or more specified
tags.
-q QUEUE, --queue QUEUE
Remove tasks on specified tasks queue or remote host
if the tasks . The queue can be defined in global or
local sos configuration file, or a file specified by
option --config. A host is assumed to be a remote
machine with process type if no configuration is
found.
-c CONFIG, --config CONFIG
A configuration file with host definitions, in case
the definitions are not defined in global sos
config.yml files.
-v {0,1,2,3,4} Output error (0), warning (1), info (2), debug (3) and
trace (4) information to standard output (default to
2).
In [9]:
usage: sos convert [-h] [-v {0,1,2,3,4}]
{sos-ipynb,ipynb-sos,ipynb-html,ipynb-pdf,ipynb-md,ipynb-ipynb,rmd-ipynb,rmd-html,sos-html}
...
Converts .sos to various formats including .html for web display, to jupyter
notebook (.ipynb), and to terminal for syntax highlighted viewing on terminal.
It also allows converting from jupyter notebook (.ipynb) to sos script (.sos).
optional arguments:
-h, --help show this help message and exit
-v {0,1,2,3,4}, --verbosity {0,1,2,3,4}
Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
converters (name of converter is not needed from command line):
{sos-ipynb,ipynb-sos,ipynb-html,ipynb-pdf,ipynb-md,ipynb-ipynb,rmd-ipynb,rmd-html,sos-html}
sos-ipynb Convert a sos script to Jupyter notebook (.ipynb) so
that it can be opened by Jupyter notebook.
ipynb-sos Export Jupyter notebook with a SoS kernel to a .sos
file. The cells are presented in the .sos file as cell
structure lines, which will be ignored if executed in
batch mode
ipynb-html Export Jupyter notebook with a SoS kernel to a .html
file. Additional command line arguments are passed
directly to command "jupyter nbconvert --to html" so
please refer to nbconvert manual for available
options.
ipynb-pdf Export Jupyter notebook with a SoS kernel to a .pdf
file. Additional command line arguments are passed
directly to command "jupyter nbconvert --to pdf" so
please refer to nbconvert manual for available
options.
ipynb-md Export Jupyter notebook with a SoS kernel to a
markdown file. Additional command line arguments are
passed directly to command "jupyter nbconvert --to
markdown" so please refer to nbconvert manual for
available options.
ipynb-ipynb Export a Jupyter notebook with a non-SoS kernel to a
SoS notebook with SoS kernel, or from a SoS notebook
to a regular notebook with specified kernel, or
execute a SoS notebook.
rmd-ipynb Export a Rmarkdown file kernel to a SoS notebook. It
currently only handles code block and Markdown, and
not inline expression.
rmd-html Export a Rmarkdown file kernel to a SoS report. It
currently only handles code block and Markdown, and
not inline expression.
sos-html Convert sos file to html format with syntax
highlighting, and save the output either to a HTML
file or view it in a broaser.
Extra command line argument could be specified to customize the style of html,
markdown, and terminal output.
Please refer to the File Conversion tutorial for more details about this command.
In [10]:
usage: sos config [-h] [-s | --hosts | -c CONFIG_FILE]
[--get [OPTION [OPTION ...]] | --unset OPTION [OPTION ...] |
--set KEY VALUE [KEY VALUE ...]] [-v {0,1,2,3,4}]
Displays configurations in host, global, local, and user specified
configuration files.
optional arguments:
-h, --help show this help message and exit
-s, --site Set (--set) or unset (--unset) options in system site
configuration file (${SOS}/site_config.yml).
--hosts Set (--set) or unset (--unset) options in hosts
(~/.sos/hosts.yml)
-c CONFIG_FILE, --config CONFIG_FILE
Set (--set) or unset (--unset) options in user
specified configuration file, or display options
(--get) also in this file.
--get [OPTION [OPTION ...]]
Display values of options that contain one of the
specified words from all configuration files.
--unset OPTION [OPTION ...]
Unset (remove) settings for specified options. The
arguments of this option can be a single configuration
option or a list of option. Wildcard characters are
allowed to match more options (e.g. '*timeout', or '*'
for all options, quotation is needed to avoid shell
expansion).
--set KEY VALUE [KEY VALUE ...]
--set KEY VALUE sets VALUE to variable KEY. The value
can be any valid python expression (e.g. 5 for integer
5 and '{"c": 2, "d": 1}' for a dictionary) with
invalid expression (e.g. val without quote) considered
as string. Syntax 'A.B=v' can be used to add {'B': v}
to dictionary 'A', and --set KEY VALUE1 VALUE2 ...
will create a list with multiple values.
-v {0,1,2,3,4}, --verbosity {0,1,2,3,4}
Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
Please refer to section SoS Syntax for details about this command.
In [11]:
usage: sos remove [-h] [-t | -u | -s | -z | -p] [-e] [--size SIZE] [--age AGE]
[-n] [-y] [-v {0,1,2,3,4}]
[FILE_OR_DIR [FILE_OR_DIR ...]]
Remove specified files and/or their signatures
positional arguments:
FILE_OR_DIR Files and directories to be removed. Directories will
be scanned for files to removed but no directory will
be removed.
optional arguments:
-h, --help show this help message and exit
-t, --tracked Limit files to only files tracked by SoS, namely files
that are input, output, or dependent files of steps.
-u, --untracked Limit files to untracked files, namely files that are
not tracked by SoS steps.
-s, --signature Remove signatures of specified files (not files
themselves). As a special case, all local signatures
will be removed if this option is specified without
target.
-z, --zap Replace files with their signatures. The file will not
be regenerated by SoS unless is it actually needed by
other steps. This option is usually used to remove
large intermediate files from completed workflows
while allowing relevant steps to be skipped during re-
execution of the workflow.
-p, --placeholders Remove placeholder files that might have been left
uncleaned after an interrupted dryrun.
-e, --external By default the remove command will only remove files
and signatures under the current project directory.
This option allows sos to remove files and/or
signature of external files.
--size SIZE Limit to files that exceed or smaller than specified
size. Value of option should be in unit K, M, KB, MB,
MiB, GB, etc, with optional prefix + for larger than
(default), or - for smaller than specified size.
--age AGE Limit to files that are modified more than (default)
or within specified age. Value of this parameter can
be in units s (second), m (minute), h (hour), or d
(day, default), or in the foramt of HH:MM:SS, with
optional prefix + for older (default) and - for newer
than specified age.
-n, --dryrun List files or directories to be removed, without
actually removing them.
-y, --yes Remove files without confirmation, suitable for batch
removal of files.
-v {0,1,2,3,4}, --verbosity {0,1,2,3,4}
Output error (0), warning (1), info (2) and debug (3)
information to standard output (default to 2). More
debug information could be generated by setting
environmental variable SOS_DEBUG to comma separated
topics of GENERAL, WORKER, CONTROLLER, STEP, VARIABLE,
EXECUTOR, TARGET, ZERONQ, TASK, DAG, and ACTION, or
ALL for all debug information
Please refer to the tutorial on Project Management for details about this command.