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        "description": "<p align=\"center\">\n  <a href=\"https://github.com/guillermo-carrasco/bcbio-nextgen-monitor\">\n    <img width=\"370\" height=\"200\" src=\"artwork/logo-letters.png\"/>\n  </a>\n</p>\n\n[![PyPI version](https://badge.fury.io/py/bcbio_monitor.svg)](https://badge.fury.io/py/bcbio_monitor)\n[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io)\n\n![Screenshot](docs/images/monitor.png)\n\n### What is this?\n[bcbio-nextgen][bcbio] is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.\n\n**bcbio-monitor** is an independent web application to track `bcbcio-nextgen` analyses.\n\nGoing to the point, you only tell `bcbio-monitor` where [bcbio-nextgen-debug.log][bcbio-logging] is (either in your local machine or on a remote server), and it'll do the work.\n\n**For a technical overview of bcbio-monitor**, please read [this][tech-post] blog post.\n\n### Quick start\n\nWith pip:\n\n    pip install bcbio_monitor\n    wget https://raw.githubusercontent.com/guillermo-carrasco/bcbio-nextgen-monitor/master/tests/data/bcbio-nextgen-debug.log\n    bcbio_monitor bcbio-nextgen-debug.log --title \"Test bcbio-monitor\"\n\nWith [conda][conda]:\n\n    conda install -c bioconda bcbio_monitor\n    wget https://raw.githubusercontent.com/guillermo-carrasco/bcbio-nextgen-monitor/master/tests/data/bcbio-nextgen-debug.log\n    bcbio_monitor bcbio-nextgen-debug.log --title \"Test bcbio-monitor\"\n\n\nRun `bcbio_monitor -h` to get information about usage. Please don't hesitate to [open an issue][issue] if something is not clear.\n\n#### Configuration\nbcbio-monitor expects a configuration file in [yaml][yaml] format to be located in `~/.bcbio/monitor.yaml`. There are two main sections that you may want to consider, those are\n`flask` and `remote`.\n\n* In `server` section, you set [configuration parameters][flask_config] for the Flask app that runs the server.\n* In `remote` server, you specify connection parameters for the machine where the logfile to read is located. **Note** that if this section is missing, bcbio-monitor will try to read the\nlogfile locally (which can also be useful for finished analysis).\n\nA working example of configuration file would be like this:\n\n```yaml\nserver:\n    SERVER_NAME: localhost:5000 # This is the address where bcbio_monitor will be served\n    DEBUG: False\n\nremote:\n    host: <remote hostname>\n    port: <SSH port> # Optional\n    username: <remote username>\n    password: <remote user password> # Optional\n```\n\nYou can also modify the logging level by adding the corresponding section in the same configuration file:\n\n```yaml\nlog:\n    level: INFO # or WARN, ERROR, DEBUG\n```\n\nLogging level is `INFO` by default.\n\n\n[bcbio]: https://bcbio-nextgen.readthedocs.org/en/latest/\n[bcbio-logging]: https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#logging\n[tech-post]: http://mussol.org/2015/11/11/bcbio-monitor/\n[issue]: https://github.com/guillermo-carrasco/bcbio-nextgen-monitor/issues/new\n[yaml]: http://yaml.org/\n[flask_config]: http://flask.pocoo.org/docs/0.10/config/#builtin-configuration-values\n[conda]: http://docs.continuum.io/anaconda/index\n",
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