where the commandline arguments are explained as follows:
```
...
...
@@ -129,6 +129,7 @@ Jobs submitted to RAREFAN are processed by redis. In your conda environmont, ins
$> conda install rq redis
```
```python
importos
...
...
@@ -158,6 +159,7 @@ class Config(object):
To launch the server, run
```
$> rq worker rarefan & # Launch a redis worker.
$> flask run
```
...
...
@@ -166,6 +168,50 @@ And navigate your browser to http://localhost:5000 .
#### NOTE
Data visualisation on a local deployment server is currently not working.
### Server notes (applies mostly to rarefan.evolbio.mpg.de production server)
#### Code updates
After a code update, the server components need to be restarted.
1. Recompile java
```console
$>cd REPINecology/REPINecology
$> gradle build
$>cd -
```
1. Restart python webserver
If the python code is installed in a conda (recommended), it should be activated since the server script depends on the `$CONDA_PREFIX` variable pointing to the environments root directory.
```console
$>sudo service rarefan restart
```
1. Restart R
Deactivate the conda environment
```console
$> conda deactivate
$>sudo service shiny-server restart
```
#### Dependency updates
Sometimes, new code also adds new software dependencies.
1. python
Simply update your conda environment
```console
$> conda env update --file=environment.yml
```
Then restart the webserver as discussed above.
1. R
Deactivate conda env and install new packages as root:
```console
$> conda deactivate
$>sudo-i
#> R
>install.packages("<new package name>")
>exit
#>exit
$>
```
Then restart shiny-server as discussed above.
## Testing
The directory *test/scripts/* contains two scripts: