Resolwe SDK for Python¶
Resolwe SDK for Python supports interaction with Genialis Server. Genialis Server is based on Resolwe workflow engine and its plugin Resolwe Bioinformatics. You can use it to upload and inspect biomedical data sets, contribute annotations and run analysis.
Install from PyPI:
pip install resdk
If you use macOS, be aware that the version of Python shipped with the system doesn’t support TLSv1.2, which is required for connecting to any Genialis Server (and probably others). To solve the issue, install the latest version of Python 3.6+ via official installer from Python.org or with Homebrew.
If you would like to contribute to the SDK code base, follow the installation steps for developers.
We will download a sample containing raw sequencing reads that were aligned to a genome:
import resdk # Create a Resolwe object to interact with the server res = resdk.Resolwe(url='https://app.genialis.com') # Enable verbose logging to standard output resdk.start_logging() # Get sample meta-data from the server sample = res.sample.get('resdk-example') # Download files associated with the sample sample.download()
Multiple files (fastq, fastQC report, bam, bai…) have downloaded to the working directory. Check them out. To learn more about the Resolwe SDK continue with Tutorials.
If you have problems connecting to our server, please contact us at firstname.lastname@example.org.
- Getting started
- SDK Reference