michaelfranklin/strelka repository overview

⁠Highlights:

• strelka/bin is exported in path
• Just call configureStrelka[Germline | Somatic]Workflow.py (and then ./runWorkflow.py)

⁠Introduction

Strelka2 is a germline and somatic small variant caller. This Dockerfile was constructed based on the install instructions⁠. Please visit the Github page for illumina/strelka⁠ for more information.

The creation and publication of this Docker container is based on required GPL3 license (at time of publishing), more information can be found on the illumina/strelka's license page⁠.

For transparency, Strelka is installed to the /opt/strelka/ directory, and the bin directory (/opt/strelka/bin) has been added to $PATH. This means you can call configureStrelkaGermlineWorkflow.py, configureStrelkaSomaticWorkflow.py or one of the two workflow demos: runStrelka[Germline | Somatic]WorkflowDemo.bash.

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Other versions of this tool can be created by changing the STRELKA_VERSION environment variable within the Dockerfile.

This Dockerfile uses ubuntu:16.04⁠ as a base as it's the highest supported version that's listed in the [docs]https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/installation.md#operating-system-guidelines⁠). There was no reason for Ubuntu over Centos.

⁠Want to test?

Just run: docker run -it michaelfranklin/strelka:2.9.10

And then within the container: configureStrelka[Germline | Somatic]Workflow.py