Documentation – Usage
Command line interface usage
Command line commands
Command line commands do not run the actual script but provide common functionality.
--help
Print help and exit.
--resolveDependencies
Download and unpack all required external tools and exit. Calling a script with
this flag is not required because all external tools will be downloaded and
unpacked automatically whenever they are required and not yet available.
--proposePrefix [input filenames]
Propose a prefix based on the input filenames specified and exit.
---yamlInfo
Print YAML-formatted script information. This switch is used by the Proteomatic
GUI to create the graphical user interface.
---yamlInfo --short
Print the script title, group and description in YAML format.
Command line options
Scripts are called using the following pattern:
./script.rb [options/parameters] [input files]
Of course, the interpreter may also be explicitly specified.
ruby script.rb [options/parameters] [input files]
Command line options must be specified before the input filenames but can be mixed with script parameters.
--applyProfile [filename]
Apply the specified parameter profile. Profiles are YAML-formatted files (ending on .pp) which contain user-defined settings of values. They can be created using the Proteomatic GUI.
--extToolsPath [path]
Use the specified path for external tools. If not specified, external tools are managed in the ext/ folder.
--useFileTracker [host:port]
Send a filetracker report to the filetracker specified upon successful completion of a script.
Filetracker
The filetracker is a TCP server which collects reports about successfully finished scripts. To start the filetracker daemon, type:
$ cd filetracker
$ ruby filetrackerd.rb localhost 7777
By default, the filetracker listens on localhost:5555, but a different host and port can be specified as shown in the example above. Use sudo and/or nohup to permanently run the filetracker on a dedicated server.
If a script is called with the --useFileTracker
switch:
$ ruby md5sum.rb --useFileTracker localhost:7777 ~/Desktop/ukca.pdf
Digesting 1 file...
The determined MD5 is 3bd0b56aa948a7eb3153e03eac00f45d
Execution took 0.0 seconds.
Submitting run to file tracker at localhost:7777... done.
…it can be seen that at the end, the report is sent to the filetracker. The filetracker daemon collects reports in monthly archives (archive/filetracker-reports-yyyy-mm.yaml).
In this example, the following report has been archived:
--- run: stdout: | Digesting 1 file... The determined MD5 is 3bd0b56aa948a7eb3153e03eac00f45d end_time: 2011-01-16 20:32:50.718015 +01:00 parameters: - Expected MD5: "" - Output directory: "" - Output file prefix: "" script_uri: md5sum.rb version: develop script_title: Check MD5 sums host: vaka user: michael start_time: 2011-01-16 20:32:50.701510 +01:00 files: - size: 78066 basename: ukca.pdf directory: /home/michael/Desktop mtime: 2010-12-26 21:54:59 +01:00 ctime: 2010-12-26 21:54:59 +01:00 input_file: true md5: 3bd0b56aa948a7eb3153e03eac00f45d
It can be seen that extensive information about input and output files is collected, including file MD5 checksums. Although a user interface for querying the filetracker with result files is not yet implemented, this setup will allow for reconstruction of entire processing pipelines at a later stage.