Monitor the status of bcbio-nextgen analyses
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README.md

PyPI version bioconda-badge

Screenshot

What is this?

bcbio-nextgen is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

bcbio-monitor is an independent web application to track bcbcio-nextgen analyses.

Going to the point, you only tell bcbio-monitor where bcbio-nextgen-debug.log is (either in your local machine or on a remote server), and it'll do the work.

For a technical overview of bcbio-monitor, please read this blog post.

Quick start

With pip:

pip install bcbio_monitor
wget https://raw.githubusercontent.com/guillermo-carrasco/bcbio-nextgen-monitor/master/tests/data/bcbio-nextgen-debug.log
bcbio_monitor bcbio-nextgen-debug.log --title "Test bcbio-monitor"

With conda:

conda install -c bioconda bcbio_monitor
wget https://raw.githubusercontent.com/guillermo-carrasco/bcbio-nextgen-monitor/master/tests/data/bcbio-nextgen-debug.log
bcbio_monitor bcbio-nextgen-debug.log --title "Test bcbio-monitor"

Run bcbio_monitor -h to get information about usage. Please don't hesitate to open an issue if something is not clear.

Configuration

bcbio-monitor expects a configuration file in yaml format to be located in ~/.bcbio/monitor.yaml. There are two main sections that you may want to consider, those are flask and remote.

  • In server section, you set configuration parameters for the Flask app that runs the server.
  • 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 logfile locally (which can also be useful for finished analysis).

A working example of configuration file would be like this:

server:
    SERVER_NAME: localhost:5000 # This is the address where bcbio_monitor will be served
    DEBUG: False

remote:
    host: <remote hostname>
    port: <SSH port> # Optional
    username: <remote username>
    password: <remote user password> # Optional

You can also modify the logging level by adding the corresponding section in the same configuration file:

log:
    level: INFO # or WARN, ERROR, DEBUG

Logging level is INFO by default.