Command reference

moa !

Assign the last issued command to “process” parameter

Usage:

moa !

Description:

Set the process parameter to the last issued command. If a moa job exists in the current directory, then the process parameter is set without questions. (even if the Moa job in question does not use the process parameter). If no moa job exists, a simple job is created first.

Note: This works only when using bash and if moainit is sourced properly. moainit defines a bash function _moa_prompt that is called every time a command is issued (using $PROMPT_COMMAND). The _moa_prompt function takes the last command from the bash history and stores it in ~/.config/moa/last.command. Additionally, the _moa_prompt function stores all commands issued in a Moa directory in .moa/local_bash_history.

moa archive

Archive a job,

Description:

Archive a job, or tree with jobs for later execution.

This command stores only those files that are necessary for execution of this job, that is: templates & configuration. In & output files, and any other file are ignored. An exception to this are all files that start with ‘moa.’

Usage:

moa archive

or:

moa archive [NAME]

an archive name can be omitted when the command is issued in a directory with a moa job, in which case the name is derived from the jobid parameter

It is possible to run this command recursively with the -r parameter - in which case all (moa job containing) subdirectories are included in the archive.

As an alternative application you can specify the –template.

moa blog

Maintain a blog (blog.md)

Usage:

moa blog

Description:

Allows a user to maintain a blog for this job (in Blog.md).

Use it as follows:

$ moa blog
Enter your blog message (ctrl-d on an empty line to finish)

... enter your message here ..

[ctrl-d]

Note: the ctrl-d needs to be given on an empty line. The text is appended to moa.desciption. In the web interface this is converted to Markdown.

moa change

Maintain a changelog file (changelog.md)

Usage:

moa blog

Description:

Allows a user to enter a short note that is appended to Changelog.md (including a timestamp). Use it as follows:

$ moa change
Enter your changelog message (ctrl-d on an empty line to finish)

... enter your message here ..

[ctrl-d]

Note: the ctrl-d needs to be given on an empty line. The text is appended to moa.desciption. In the web interface this is converted to Markdown.

moa cp

Copy a moa job

Description:

Copy a moa job, or a tree with jobs.

moa cp copies only those files defining a job: the template files and the job configuration. Additionaly, all files in the moa directory that start with moa. (for example moa.description are copied as well. Data and log files are not copied!

The command has two modes of operation. The first is:

moa cp 10.from 20.to

copies the moa job in 10.from to a newly created 20.to directory. If the 20.to directory already exists, a new directory is created in 20.to/10.from. As an shortcut one can use:

moa cp 10.from 20

in which case the job will be copied to the 20.from directory.

If the source (10.from) directory is not a Moa job, the command exits with an error.

The second mode of operation is recursive copying:

moa cp -r 10.from 20.to

in which case all subdirectories under 10.from are traversed and copied - if a directory contains a Moa job.

::TODO.. Warn for changing file & dir links

moa err

Returns stderr of the last moa run

moa files

Show an overview of the files for this job

Description:

moa files - Display discovered & inferred files for this job

Usage:

moa files

Display a list of all files discovered (for input & prerequisite type filesets) and inferred from these for map type filesets.

moa gitadd

Add the current job to the git repository

Description:

Add a job to the git repository

moa gitlog

display a nicely formatted git log

Description:

Print a log to screen

moa gittag

Tag the current version

moa help

Display help for a template

moa kill

Kill a job

Description:

See if a job is running, if so - kill it

moa list

Print a list of all known templates

Description:

moa list - Print a list of all known templates

Usage:

moa list
moa list -l

Print a list of all templates known to this moa installation. If the option ‘-l’ is used, a short description for each tempalte is printed as well.

moa lock

Lock this job - prevent execution

moa log

Show the logs for this job

Description:

moa lcog - show a log of the most recent moa calls

Usage:

moa log [LINES]

Shows a log of moa commands executed. Only commands with an impact on the pipeline are logged, such as moa run & moa set. The number of log entries to display can be controlled with the optional LINES parameter.

moa map

Create a “map” adhoc analysis

Usage:

moa map -t "title" -- echo "do something"

Description:

Anything after – will be stored in the process variable. If – is omitted, Moa will query the user.

Moa will also query the user for input & output files. An example session:

$ moa map -t 'test map'
process:
> echo 'processing {{ input }} {{ output }}'
input:
> ../10.input/*.txt
output:
> ./*.out

Assuming you have a number of *.txt files in the ../10/input/ directory, you will see, upon running:

processing ../10.input/test.01.txt ./test.01.out
processing ../10.input/test.02.txt ./test.02.out
processing ../10.input/test.03.txt ./test.03.out
...

If the output file exists, and is newer than the input file, the process will not be executed for that specific pair. If you need the job to be repeated, you should either delete the output files or touch the input files.

moa mv

Rename/renumber/move a job

Description:

Renumber or rename a moa job..

moa new

Create a new Moa job

Description:

moa new

Usage:

moa new TEMPLATE_NAME -t 'a descriptive title'

moa out

Returns stdout of the last moa run

moa pause

Pause a job

Description:

pause a running job

moa postcommand

Run the postcommand

Usage:

moa postcommand

Description:

Execute the postcommand

moa precommand

Run the precommand

Usage:

moa pprecommand

Description:

Execute the precommand

moa readme

Edit the Readme.md file for this job

Usage:

moa readme

Description:

Edit the Readme.md file - you could, obviously, also edit the file yourself.

moa reduce

Create a “reduce” adhoc analysis

Usage:

moa reduce -t "title" -- echo "do something"

Description:

Create a ‘reduce’ adhoc job.

There are a number of ways this command can be used:

$ moa reduce -t 'a title' -- echo 'define a command'

Anything after – will be the executable command. If omitted, Moa will query the user for a command.

Moa will also query the user for input & output files. An example session:

$ moa map -t 'something intelligent'
process:
> echo 'processing {{ input }} {{ output }}'
input:
> ../10.input/*.txt
output:
> ./*.out

Assuming you have a number of text files in the ../10/input/ directory, you will see, upon running:

processing ../10.input/test.01.txt ./test.01.out
processing ../10.input/test.02.txt ./test.02.out
processing ../10.input/test.03.txt ./test.03.out
...

moa refresh

Reload the template

Description:

Refresh the template - i.e. reload the template from the central repository.

moa report

generate a report for this job

moa resume

Resume a job

Description:

pause a running job

moa set

Set, change or remove variables

Usage:

moa set [KEY] [KEY=VALUE]

Description:

This command can be used in a number of ways:

moa set PARAMETER_NAME=PARAMETER_VALUE
moa set PARAMETER_NAME='PARAMETER VALUE WITH SPACES'
moa set PARAMETER_NAME

In the first two forms, moa sets the parameter PARAMETER_NAME to the PARAMETER_VALUE. In the latter form, Moa will present the user with a prompt to enter a value. Note that the first two forms the full command lines will be processed by bash, which can either create complications or prove very useful. Take care to escape variables that you do not want to be expandend and use single quotes where you can.

moa show

Show configuration

Usage:

moa show

Description:

Show all parameters know to this job. Parameters in bold are specifically configured for this job (as opposed to those parameters that are set to their default value). Parameters in red are not configured, but need to be for the template to operate. Parameters in blue are not configured either, but are optional.

moa simple

Create a “simple” adhoc analysis

Usage:

moa simple -t "title" -- echo "do something"

Description:

Create a ‘simple’ adhoc job. Simple meaning that no in or output files are tracked.

There are a number of ways this command can be used:

moa simple -t 'a title' -- echo 'define a command'

Anything after – will be the executable command. Note that bash will attempt to process the command line. A safer method is:

moa simple -t 'a title'

Moa will query you for a command to execute (the parameter process).

moa status

Show the state of the current job

Description:

moa status - print out a status status message

Usage:

moa status

moa test

Test the currennt configuration

moa tree

display a directory tree

moa unittest

Run Moa unittests

moa unlock

Unlock this job

moa unset

Remove a variable

Usage:

moa unset KEY

Description:

Remove a configured parameter from this job. In the parameter was defined by the job template, it reverts back to the default value. If it was an ad-hoc parameter, it is lost from the configuration.

moa version

Print the moa version

Description:

moa version - Print the moa version number

msp

moa set process

Usage:

msp

this is an alias for the often used:

moa set process