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        "author": "Datirium, LLC",
        "author_email": "support@datirium.com",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Environment :: Other Environment",
            "Intended Audience :: Developers",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Natural Language :: English",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: Microsoft :: Windows :: Windows 10",
            "Operating System :: Microsoft :: Windows :: Windows 8.1",
            "Operating System :: OS Independent",
            "Operating System :: POSIX",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Scientific/Engineering :: Information Analysis",
            "Topic :: Scientific/Engineering :: Medical Science Apps."
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        "description": "# BioWardrobe backend (airflow+cwl)\n\n### About\nPython package to replace [BioWardrobe's](https://github.com/Barski-lab/biowardrobe) python/cron scripts. It uses\n[Apache-Airflow](https://github.com/apache/incubator-airflow)\nfunctionality with [CWL v1.0](http://www.commonwl.org/v1.0/).\n\n### Install\n1. Add biowardrobe MySQL connection into Airflow connections\n    ```sql\n    select * from airflow.connection;\n    insert into airflow.connection values(NULL,'biowardrobe','mysql','localhost','ems','wardrobe','',null,'{\"cursor\":\"dictcursor\"}',0,0);\n    ```\n2. Install\n    ```sh\n    sudo pip3 install .\n    ```\n\n### Requirements\n1. Make sure your system satisfies the following criteria:\n      - Ubuntu 16.04.3\n        - python3.6\n            ```sh\n            sudo add-apt-repository ppa:jonathonf/python-3.6\n            sudo apt-get update\n            sudo apt-get install python3.6\n            ```\n        - pip3\n          ```sh\n          curl https://bootstrap.pypa.io/get-pip.py | sudo python3.6\n          pip3 install --upgrade pip3\n          ```\n        - setuptools\n          ```sh\n          pip3 install setuptools\n          ```\n        - [docker](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/)\n          ```sh\n          sudo apt-get update\n          sudo apt-get install apt-transport-https ca-certificates curl software-properties-common\n          curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -\n          sudo add-apt-repository \"deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable\"\n          sudo apt-get update\n          sudo apt-get install docker-ce\n          sudo groupadd docker\n          sudo usermod -aG docker $USER\n          ```\n          Log out and log back in so that your group membership is re-evaluated.\n        - libmysqlclient-dev\n          ```sh\n          sudo apt-get install libmysqlclient-dev\n          ```\n        - nodejs\n          ```sh\n          sudo apt-get install nodejs\n          ```\n2. Get the latest version of `cwl-airflow-parser`.\n   If **[Apache-Airflow](https://github.com/apache/incubator-airflow)**\n   or **[cwltool](http://www.commonwl.org/ \"cwltool main page\")** aren't installed,\n   installation will be done automatically with recommended versions. Set `AIRFLOW_HOME` environment \n   variable to airflow config directory default is `~/airflow/`.\n      ```sh\n      git clone https://github.com/datirium/cwl-airflow-parser.git\n      cd cwl-airflow-parser\n      sudo pip3 install .\n      ```\n\n3. If required, add **[extra airflow packages](https://airflow.incubator.apache.org/installation.html#extra-packages)**\n   for extending Airflow functionality, for instance, with MySQL support `pip3 install apache-airflow[mysql]`.\n\n### Running\n\n1. To create BioWardrobe's dags run `biowardrobe-init` in airflow's dags directory \n    ```\n    cd ~/airflow/dags\n    ./biowardrobe-init \n    ```\n2. Run Airflow scheduler:\n   ```sh\n   airflow scheduler\n   ```\n3. Use `airflow trigger_dag` with input parameter `--conf \"JSON\"` where JSON is either job definition or biowardrobe_uid \nand explicitly specified cwl descriptor `dag_id`.\n    ```sh\n    airflow trigger_dag --conf \"{\\\"job\\\":$(cat ./hg19.job)}\" \"bowtie-index\"\n    ```\n    where `hg19.job` is:\n    ```json\n    {\n      \"fasta_input_file\": {\n        \"class\": \"File\", \n        \"location\": \"file:///wardrobe/indices/bowtie/hg19/chrM.fa\", \n        \"format\":\"http://edamontology.org/format_1929\",\n        \"size\": 16909,\n        \"basename\": \"chrM.fa\",\n        \"nameroot\": \"chrM\",\n        \"nameext\": \".fa\"\n      },\n      \"output_folder\": \"/wardrobe/indices/bowtie/hg19/\",\n      \"threads\": 6,\n      \"genome\": \"hg19\"\n    }\n    ```\n\n4. All the output will be moved from temporary directory into **output_folder** parameter\n  of the job.",
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        "name": "biowardrobe-airflow-analysis",
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