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    "info": {
        "author": "Ben Taylor",
        "author_email": "ben.taylor@sanger.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: System :: Monitoring",
            "Topic :: Utilities"
        ],
        "description": "Pathogen Pipeline Configuration Tools (path\\_pipe\\_conf\\_tools)\n===============================================================\n\nThis is probably not very interesting unless you work in the pathogen\ninformatics team at the Wellcome Trust Sanger Institute and almost\ncertainly not it you don't use `the vr-pipe\npipeline <https://github.com/VertebrateResequencing/vr-pipe>`_.\n\nGiven a config directory, this script finds all of the\n``*_pipeline.conf`` files in the directory and its immediate children.\nIt parses these files and outputs their contents in json. This is either\nsaved to a file or stdout.\n\nThis is used in collaboration with\n`jsontoemail <https://github.com/sanger-pathogens/jsontoemail>`_ and a\n``cron`` job to send updates / reminders to the pathogen informatics\nteam.\n\nUsage\n-----\n\n::\n\n    $ list-pathogen-pipeline-jobs -h\n    usage: list-pathogen-pipeline-jobs [-h] [--output_file OUTPUT_FILE] config_dir\n\n    Outputs details of all of the pathogen jobs in the pipeline\n\n    positional arguments:\n      config_dir            Config directory to be searched for job trackers (also\n                            searches child dircectories)\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --output_file OUTPUT_FILE, -o OUTPUT_FILE\n                            File to output results to (defaults to stdout)\n\nExample output\n--------------\n\n::\n\n    {\n      \"created_at\": \"2015-03-24T15:26:17.246253\",\n      \"jobs\": [\n        {\n          \"approval_required\": true,\n          \"config_file\": \"/parent_dir/assembly_jobs/job_1.conf\",\n          \"job_type\": \"__Assembly__\",\n          \"pipeline_tracker\": \"/parent_dir/assembly_job_tracker.conf\"\n        },\n        {\n          \"approval_required\": true,\n          \"config_file\": \"/parent_dir/assembly_jobs/job_2.conf\",\n          \"job_type\": \"__Assembly__\",\n          \"pipeline_tracker\": \"/parent_dir/assembly_job_tracker.conf\"\n        },\n        {\n          \"approval_required\": false,\n          \"config_file\": \"/parent_dir/assembly_jobs/job_3.conf\",\n          \"job_type\": \"__Assembly__\",\n          \"pipeline_tracker\": \"/parent_dir/assembly_job_tracker.conf\"\n        },\n        {\n          \"approval_required\": true,\n          \"config_file\": \"/parent_dir/annotation_jobs/job_1.conf\",\n          \"job_type\": \"__Annotation__\",\n          \"pipeline_tracker\": \"/parent_dir/annotation_job_tracker.conf\"\n        },\n        {\n          \"approval_required\": false,\n          \"config_file\": \"/parent_dir/mapping_jobs/job_1.conf\",\n          \"job_type\": \"__Mapping__\",\n          \"pipeline_tracker\": \"/parent_dir/mapping_job_tracker.conf\"\n        },\n        {\n          \"approval_required\": false,\n          \"config_file\": \"/parent_dir/mapping_jobs/job_2.conf\",\n          \"job_type\": \"__Mapping__\",\n          \"pipeline_tracker\": \"/parent_dir/mapping_job_tracker.conf\"\n        }\n      ]\n    }\n\nTesting\n-------\n\n::\n\n    ./run_tests.sh\n\nDependencies\n------------\n\nTests require: \n\n- mock\n\npath\\_pipe\\_conf\\_tools has been tested on Ubuntu 12.04 with python\n2.7.3",
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        "keywords": null,
        "license": "GPLv3",
        "maintainer": null,
        "maintainer_email": null,
        "name": "path_pipe_conf_tools",
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        "summary": "Tools for working with the pathogen pipeline at The Wellcome Trust Sanger Institute",
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