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Script of Scripts (SoS) consists of SoS Notebook, a Jupyter-based polyglot notebook that allows the use of multiple Jupyter kernels in one notebook, and SoS Workflow, a workflow system for the execution of workflows in both process- and outcome-oriented styles. It is designed for data scientists and bioinformatics who routinely work with scripts in different languages such as bash, Python, R, and SAS. This repository contains the SoS Workflow workflow engine.

Please refer to relevant publications SoS Notebook: An Interactive Multi-Language Data Analysis Environment in Bioinformatics, Script of Scripts: a pragmatic workflow system for daily computational research in PLoS Computational Biology, and the SoS homepage for more information on SoS Notebook and SoS Workflow.

We welcome and value community contributions: please post issues to provide us feedback or get our support; please send pull requests if you have helped fixing bugs or making improvements to the source code. In addition, if you are interesting in extending SoS, for example adding a new target type or task engine, please have a look at our tutorial on extending SoS here.

Installing SoS Workflow and Notebook

Change Log of SoS Workflow and SoS Notebook

SoS 0.25.1:

SoS 0.25.0:

SoS 0.24.5:

SoS 0.22.5:

SoS Notebook 0.22.3

SoS Notebook 0.22.2

SoS 0.21.12

SoS 0.20.9

SoS 0.19.15

SoS 0.19.0

SoS Notebook 0.18.5

SoS 0.18.6

SoS 0.18.5

SoS 0.18.4

SoS Notebook 0.18.1

SoS 0.18.0

SoS Notebook 0.18.0

SoS 0.9.16.10

SoS 0.9.16.0, SoS Notebook 0.9.16.0

SoS 0.9.15.1

SoS 0.9.14.10

SoS 0.9.14.3:

SoS Notebook 0.9.14.4:

SoS Notebook 0.9.14.1

SoS 0.9.14.1

SoS Notebook 0.9.13.4

SoS Notebook 0.9.12.12

SoS 0.9.12.11

SoS Notebook 0.9.12.11

SoS 0.9.12.9

SoS Notebook 0.9.12.9

SoS 0.9.12.3

SoS 0.9.11.3

SoS 0.9.11.2

SoS 0.9.10.19

SoS Notebook 0.9.10.17