Metadata-Version: 1.1
Name: path_pipe_conf_tools
Version: 0.0.2
Summary: Tools for working with the pathogen pipeline at The Wellcome Trust Sanger Institute
Home-page: https://github.com/sanger-pathogens/PathPipeConfTools
Author: Ben Taylor
Author-email: ben.taylor@sanger.ac.uk
License: GPLv3
Description: Pathogen Pipeline Configuration Tools (path\_pipe\_conf\_tools)
        ===============================================================
        
        This is probably not very interesting unless you work in the pathogen
        informatics team at the Wellcome Trust Sanger Institute and almost
        certainly not it you don't use `the vr-pipe
        pipeline <https://github.com/VertebrateResequencing/vr-pipe>`_.
        
        Given a config directory, this script finds all of the
        ``*_pipeline.conf`` files in the directory and its immediate children.
        It parses these files and outputs their contents in json. This is either
        saved to a file or stdout.
        
        This is used in collaboration with
        `jsontoemail <https://github.com/sanger-pathogens/jsontoemail>`_ and a
        ``cron`` job to send updates / reminders to the pathogen informatics
        team.
        
        Usage
        -----
        
        ::
        
            $ list-pathogen-pipeline-jobs -h
            usage: list-pathogen-pipeline-jobs [-h] [--output_file OUTPUT_FILE] config_dir
        
            Outputs details of all of the pathogen jobs in the pipeline
        
            positional arguments:
              config_dir            Config directory to be searched for job trackers (also
                                    searches child dircectories)
        
            optional arguments:
              -h, --help            show this help message and exit
              --output_file OUTPUT_FILE, -o OUTPUT_FILE
                                    File to output results to (defaults to stdout)
        
        Example output
        --------------
        
        ::
        
            {
              "created_at": "2015-03-24T15:26:17.246253",
              "jobs": [
                {
                  "approval_required": true,
                  "config_file": "/parent_dir/assembly_jobs/job_1.conf",
                  "job_type": "__Assembly__",
                  "pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
                },
                {
                  "approval_required": true,
                  "config_file": "/parent_dir/assembly_jobs/job_2.conf",
                  "job_type": "__Assembly__",
                  "pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
                },
                {
                  "approval_required": false,
                  "config_file": "/parent_dir/assembly_jobs/job_3.conf",
                  "job_type": "__Assembly__",
                  "pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
                },
                {
                  "approval_required": true,
                  "config_file": "/parent_dir/annotation_jobs/job_1.conf",
                  "job_type": "__Annotation__",
                  "pipeline_tracker": "/parent_dir/annotation_job_tracker.conf"
                },
                {
                  "approval_required": false,
                  "config_file": "/parent_dir/mapping_jobs/job_1.conf",
                  "job_type": "__Mapping__",
                  "pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
                },
                {
                  "approval_required": false,
                  "config_file": "/parent_dir/mapping_jobs/job_2.conf",
                  "job_type": "__Mapping__",
                  "pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
                }
              ]
            }
        
        Testing
        -------
        
        ::
        
            ./run_tests.sh
        
        Dependencies
        ------------
        
        Tests require: 
        
        - mock
        
        path\_pipe\_conf\_tools has been tested on Ubuntu 12.04 with python
        2.7.3
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: System :: Monitoring
Classifier: Topic :: Utilities
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
