Slivka Public Server and Jalview
The easiest way to start using Slivka web-services is by launching Jalview. Slivka is supported in Jalview version 2.12 onwards and users connect to our public slivka-bio server by default. To access supported services, simply launch Jalview and run any of the methods under the "Web Service" menu. If you are concerned about privacy, want to run analysis on your own hardware, or create custom services, you can setup your own Slivka server. You can then configure Jalview to use the new server by opening Jalview's preferences dialog and adding its URLs via the Slivka Services tab. If you want to use different Slivka server, navigate to Preferences menu and edit, add or remove URLs from the Slivka Services tab. If you are concerned about privacy and/or want to run analysis on your own hardware you can setup a local Slivka server in you infrastructure.
Accessing from Python/Jupyter

Slivka services can easily be accessed from a Python script or interactive console. First, install the slivka client directly from our github repository:

pip install git+https://github.com/warownia1/slivka-python-client.git
or from conda:
conda install -c mmwarowny -c conda-forge slivka-client
The package contains classes allowing services discovery as well as methods for submitting and retrieving jobs. More information about client usage is available in the documentation.

The public server is available at https://www.compbio.dundee.ac.uk/slivka/.

Setting up a slivka-bio server

If you want to deploy your own slivka-bio server, the configuration files are publicly available in our github repository and as a conda package. Configuration files and bioinformatic tools can be installed with:

conda install -c mmwarowny -c bioconda -c conda-forge slivka-bio

The slivka configuration files will be placed in $CONDA_PREFIX/var/slivka-bio/. Additionally, slivka needs access to the mongo database which can be installed locally from conda.

conda install mongodb

To finish configuring you new slivka-bio server refer to the README file located in the repository. For detailed information about how to configure slivka, its job execution systems and the types of service it provides, see the full Slivka documentation.