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
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.
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"
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"
bcbio_monitor -h to get information about usage. Please don't hesitate to open an issue if something is not clear.
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
serversection, you set configuration parameters for the Flask app that runs the server.
remoteserver, 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.