Accessing from Python/Jupyter

Slivka services can be accessed from a Python script or interactive console using the slivka client library for Python. The client can be installed from conda (recommended)

conda install -c slivka -c conda-forge slivka-client

or directly from our GitHub repository

pip install git+

The package allows convenient programmatic service discovery, job submission and retrieving output files. More information about the client usage is available in the client documentation.

The public server is available at

Setting up a slivka-bio server

In order to deploy your own slivka server, you need to install the slivka package on your machine, provide it with service configuration files and have access to a Mongo database. Make sure the database is available on your system and contact your system administrator to configure it. Alternatively, you can install and run a mongodb package from the conda-forge channel using conda.

The fastest way to automatically get slivka with configuration files and tools is by installing the slivka-bio package from our anaconda channel which bundles the slivka package, web service configuration files and bioinformatics software.

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

When using this method, the configuration files will be copied to $CONDAPREFIX/var/slivka-bio/.

If you prefer to set things up manually, install the latest slivka package from the slivka channel using conda and initialize an empty project in a new directory using slivka init command. Alternatively, you can clone the existing configuration from our slivka-bio GitHub repository. Refer to the README file located in the repository for more information or visit the complete Slivka documentation.