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.
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.
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
.
server
section, you set configuration parameters for the Flask app that runs the server.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.