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.. highlight:: yaml
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Modules
=======

A module specifies exactly one analysis that can be run within PSOT. Each
module has a default configuration that is specified in its manifest. During the
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execution, a module will run through two phases: the analysis and the conversion
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phase. The phases are implemented as commandline tools that have at least the
following parameters:

* analysis

  * ``--fasta`` - the fasta file to process
  * ``--output`` - the result file/directory

* convert
  
  * ``--result`` - the result from the analysis step
  * ``--output`` - the converted json file

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The scripts can have additional parameters. They can be set in the paramaters
section of the module manifest. The parameters can be overridden in the
profile.

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A module manifest has the following structure::

    # Module manifest for the blastp against swissprot analysis

    # The name of the module. Is needed for the list-analyses option, for custom
    # configurations and custom profiles
    name: 'blastp_swissprot'

    # Short description of the analysis
    info: 'blastp analysis against swissprot'

    # The name of the script for the analysis step. Must take a --fasta parameter
    analysis:
	script: 'run_blastp.py'
	parameters:
	    database: '/vol/biodb/uniprot/uniprot_sprot.fasta'
	    evalue: 1e-10
	    use_accession:

    # The name of the result to json converter script. Must take one parameter, the
    # result file from the analysis_script
    converter:
	script: 'convert_blastp.py'
	parameters:
	    dbxref: UniProtKB/Swiss-Prot

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