Registering a FileSet Instance

To register one or more FileSet instances, use the command plugins-register-fileset as follows:

plugins-register-fileset \
--fileset-area FILESET_AREA_LOCATION \
--owner OWNER \
--plugins-dir PLUGINS_ROOT_LOCATION \
ENTRY1 ENTRY2 ... ENTRYn

In the command line above, ENTRY* can be written with any of the following four syntaxes:

  1. FILESETID: PATH1 PATH2 … PATHn
  2. FILESETID: PATTERN1 PATTERN2 … PATTERNn
  3. PATH1 PATH2 … PATHn
  4. PATTERN1 PATTERN2 … PATTERNn

where:
– FILESETID is the ID of a FileSet configuration under the plugins root.
– PATTERN is a valid pattern with wildcards resolvable by the bash shell
– PATH is an absolute or relative path to an existing file or directory

Examples:

  • COMPACT_READS: /some/path/myfilename.compact-reads
  • COMPACT_READS: /some/path/*.compact-reads
  • GOBY_ALIGNMENTS: /some/path/*.index /some/path/*.entries /some/path/*.header
  • /some/path/*.compact-reads
  • /some/path/myfilename.compact-reads

All can be mixed, BUT you need to use the guess: keyword if you want to mix 3 or 4 with 1 or 2. For instance:

  • GOBY_ALIGNMENTS: /some/path/*.index /some/path/*.entries /some/path/*.header /another/path/R.compact-reads

will not work because the FileSet manager will try to bind R.compact-reads in the GOBY_ALIGNMENTS slot, where the .compact-reads extension is not accepted. You can work-around this in one of two ways: (1) use the guess: keyword, or (2) move R.compact-reads to the first argument position:

(1) GOBY_ALIGNMENTS: /some/path/*.index /some/path/*.entries /some/path/*.header guess: /another/path/R.compact-reads

(2) /another/path/R.compact-reads GOBY_ALIGNMENTS: /some/path/*.index /some/path/*.entries /some/path/*.header

In option (2), we avoid using the guess: keyword by changing the order of evaluation: R.compact-reads can be bound to a slot that accepts .compact-reads extension when it is at the beginning of the command line, but once the GOBY_ALIGNMENTS slot is named, this is no longer possible, so the guess: keyword must be used.

If the registration succeeded, the TAGs assigned to the newly created FileSet instances are returned. Registrations can fail when any of the input ENTRIES can’t be assigned to any FileSet plugin available in the PLUGINS_ROOT_LOCATION. When a failure occurs, FileSets registered up the the failure point are automatically unregistered, meaning that the registration policy is that either all files are successfully registered or none is.

Unregistering a FileSet Instance

To unregister a FileSet instance, use the command plugins-unregister-fileset with the following syntax:

plugins-unregister-fileset \
--fileset-area FILESET_AREA_LOCATION \
--owner OWNER \
--plugins-dir PLUGINS_ROOT_LOCATION \
--tag TAG

where:

  • TAG is the identifier of the FileSet instance to unregister.