# Pavian 1.2.0


## Pavian - interactive browser application for omics data

Pavian is a interactive browser application for analyzing and visualization
metagenomics classification results from classifiers such as Kraken, KrakenUniq,
Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for
validation of matches to a particular genome.

Location and version:

```console
$ bash
$ source /local/cluster/pavian/activate.sh
$ Rscript -e "packageVersion('pavian')"
[1] ‘1.2.0’
```

A wrapper script has been provided to facilitate the use of interactive pavian
sessions.

On vaughan:

```bash
cd /path/to/viz/dir
SGE_Batch -c 'start_pavian' -q <QUEUE> -r sge.pavian
```

Examine the stdout in the sge.pavian directory to get the `ssh` command to run
for the port tunneling to the node, then navigate your local browser to the
given url to get started. By default, the 'load dataset' tab should be in your
current working directory.

Make sure to kill the job using `qdel` when you are finished with your session.

To close the tunneled connection from your local machine, run the `ssh -S
<SOCKET_NAME> -O check .` and `ssh -S <SOCKET_NAME> -O exit .` commands as
given. You can check for already established sockets by running `ls $HOME/.ssh`
and looking for files named `<HOST>-<PORT>-pavian`.

software ref: <https://github.com/fbreitwieser/pavian>  
research ref: <https://doi.org/10.1093/bioinformatics/btz715>