Pathogen Sequencing Unit

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Glossary
  • Executable

    This represents a command line program, such as blastall or fasta. It has a name which is used to find the executable in the filesystem. Names may be simply the binary or script file name e.g. 'blastall' (in which case the PATH environment variable will be used to locate it), or an absolute path e.g. '/usr/local/bin/blastall'. A version string and description are also available for each Executable.

  • Job

    This represents a single execution of a command line program specified by an Executable. It specifies optional sources or destinations for input, output and error streams from the program to be run. Usually these will be files. It also specifies a template string which details the command line used to run the program. For batch queue submissions there are properties for queue name and batch system ID. As it runs a Job changes status from WAITING through to COMPLETED (or possibly FAILED). A Job may itself be a composite of other Jobs arranged in a tree where the goal Job is at the root and the leaf Jobs must be executed first.

  • Owner

    An Owner is the point of contact for a particular Task. Owners may be individuals or projects. However, they must always have a valid username, email address and telephone number associated with them.

  • Status

    As a Job runs it changes Status. All Jobs start as WAITING - this means that the system is not able to consider them as candidates for running. To be run a Job must be promoted to READY - this means that the system is considering the Job. The Job will then be STARTED and hopefully COMPLETED, although it may end up being FAILED if it returns a non-zero exit value or some other error occurs. There are two other Status values; CANCELLED - which indicates a user-originated cancellation request and SKIPPED - which indicates a system decision not to run a Job because it became redundant.

  • Task

    A Task is a unit of Jobs belonging to an Owner. Its Jobs are normally focussed on a particular operation which should be given in its description. Tasks also have a name which should be the same across all instances of a particular Task. A Task specifies a list of Jobs with the goal Job at the start of the list. Each Job may itself define a Job tree proceeding from leaves to root towards the goal. The root of the tree furthest from the goal implicitly links to the leaves of the next tree such that its completion allows them to be executed. The net result is a directional pipe which may be heavily parallel at any point, proceeding to a single goal.