bcbio_monitor 1.0.6

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

<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>

[](https://badge.fury.io/py/bcbio_monitor)
[](http://bioconda.github.io)


### 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