Skip to main content
Help us improve PyPI by participating in user testing. All experience levels needed!

bcbio-monitor is an extension of bcbio-nextgen to visualize its progress

Project description

<p align="center">
<a href="https://github.com/guillermo-carrasco/bcbio-nextgen-monitor">
<img width="370" height="200" src="artwork/logo-letters.png"/>
</a>
</p>

[![PyPI version](https://badge.fury.io/py/bcbio_monitor.svg)](https://badge.fury.io/py/bcbio_monitor)
[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io)

![Screenshot](docs/images/monitor.png)

### What is this?
[bcbio-nextgen][bcbio] 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][bcbio-logging] 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][tech-post] 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]:

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][issue] if something is not clear.

#### Configuration
bcbio-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
`flask` and `remote`.

* In `server` section, you set [configuration parameters][flask_config] 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:

```yaml
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:

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

Logging level is `INFO` by default.


[bcbio]: https://bcbio-nextgen.readthedocs.org/en/latest/
[bcbio-logging]: https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#logging
[tech-post]: http://mussol.org/2015/11/11/bcbio-monitor/
[issue]: https://github.com/guillermo-carrasco/bcbio-nextgen-monitor/issues/new
[yaml]: http://yaml.org/
[flask_config]: http://flask.pocoo.org/docs/0.10/config/#builtin-configuration-values
[conda]: http://docs.continuum.io/anaconda/index

Project details


Release history Release notifications

This version
History Node

1.0.6

History Node

1.0.5

History Node

1.0.2

History Node

1.0.1

History Node

1.0

History Node

0.2.0

History Node

0.1.3

History Node

0.1.1

History Node

0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
bcbio_monitor-1.0.6.tar.gz (774.6 kB) Copy SHA256 hash SHA256 Source None Nov 30, 2015

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page