Debian Science Project
Summary
Workflow
workflow management systems useful for scientific research

This task lists some packages providing workflow management systems useful for scientific research.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Workflow packages

Official Debian packages with high relevance

capsule-nextflow
packaging and deployment tool for Java applications
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A capsule is a single executable JAR that contains everything an application needs to run either in the form of embedded files or as declarative metadata. It can contain JAR artifacts, dependencies and resources, native libraries, the required Java Runtime Environment version, the Java Virtual Machine flags required to run the application well, Java or native agents and more. In short, a capsule is a self-contained JAR that knows everything there is to know about how to run the application the way it is meant to run.

One way of thinking about a capsule is as a fat JAR on steroids (that also allows native libraries and never interferes with your dependencies) and a declarative startup script rolled into one; another, is to see it is as the deploy-time counterpart to your build tool. Just as a build tool manages your build, Capsule manages the launching of your application.

This package contains a fork of the original capsule project. This fork is suited as a dependency of nextflow.

coop-computing-tools
cooperative computing tools
Maintainer: Alastair McKinstry
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uitoolkitncurses
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This is a collection of software that help users to share resources in a complex, heterogeneous, and unreliable computing environment. This includes:

  • Chirp: A personal filesystem and I/O protocol that allows unprivileged users to share space securely, efficiently, and conveniently. When combined with Parrot, Chirp allows users to create custom wide-area distributed filesystems.
  • Parrot: A transparent user-level virtual filesystem that allows any ordinary program to be attached to a remote storage device such as an FTP server or a Chirp server.
  • Makeflow: A workflow system for parallel and distributed computing that uses a language very similar to Make.
  • Work Queue: A system and API for building master-worker style programs that scale up to thousands of processors.
  • All Pairs: A computational abstraction for running very large Cartesian products.
  • Wavefront: A computational abstraction for running very large dynamic programming problems.
  • The Fault Tolerant Shell: A high-level programming language that allows users to combine the ease of shell scripting, the power of distributed programming, and the precision of compiled languages. Basically, parallel programming and exception handling for scripts.
cwltool
Referenzimplemantation der Common Workflow Language
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Dieses Paket beinhaltet die Referenzimplementierung des Common Workflow Language Standards.

Der offene Standard CWL beschreibt Analyse-Workflows und Werkzeuge mit dem Ziel der Portier- und Skalierbarkeit für eine Vielzahl von Soft- und Hardware, von Workstations bis zu Clustern, Cloud und High Performance Computing (HPC) Umgebungen. CWL wurde für die Anforderungen bei hohem Datenaufkommen entworfen, wie sie in der Bioinformatik, der medizinischen Bildverarbeitung, der Astronomie, Physik und Chemie vorkommen.

Der Anspruch der Referenzimplementierung (cwltool) ist es, alle Aspekte des Standards umzusetzen und eine vollständige Validierung von CWL-Dateien zu bieten sowie weitere Werkzeuge für das Arbeiten mit CWL-Beschreibungen.

Please cite: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reye, Bogdan Gavrilović, Carole Goble and The CWL Community: Methods included: standardizing computational reuse and portability with the Common Workflow Language. Communications of the ACM 65(6):54-63 (2022)
Registry entries: SciCrunch  Bioconda 
gearman
Distributed job queue
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buster-backports1.1.19.1+ds-2~bpo10+1all
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Gearman is a system to farm out work to other machines, dispatching function calls to machines that are better suited to do work, to do work in parallel, to load balance lots of function calls, or to call functions between languages.

This package is an empty package that depends on both the client and the server.

gearman-tools
Tools for the Gearman distributed job queue
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Gearman is a system to farm out work to other machines, dispatching function calls to machines that are better suited to do work, to do work in parallel, to load balance lots of function calls, or to call functions between languages.

This package contains some command line tools for manipulating gearman jobs.

make
Werkzeug zur Steuerung der Kompilierung
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GNU Make ist ein Hilfsprogramm, das die Erzeugung von ausführbaren und anderen Dateien aus Quelltexten steuert. Es ermittelt automatisch, welche Teile eines großen Programms (erneut) erstellt werden müssen und führt die dafür erforderlichen Befehle aus. Make lässt sich für jede Aufgabenstellung verwenden, bei der eine Reihe von »Targets« (Dateien) in Abhängigkeit von anderen Eingabedateien automatisch aktualisiert werden, wann immer diese erneuert worden sind. Dies ist nicht nur auf die Erstellung von Computerprogrammen beschränkt. In der Tat ist Make ein Allzweckwerkzeug für die Auflösung von Abhängigkeiten.

The package is enhanced by the following packages: make-doc
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pegasus-wms
Scientific workflow management system for HTCondor
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The Pegasus project encompasses a set of technologies the help workflow-based applications execute in a number of different environments including desktops, campus clusters, grids, and now clouds. Scientific workflows allow users to easily express multi-step computations, for example retrieve data from a database, reformat the data, and run an analysis. Once an application is formalized as a workflow the Pegasus Workflow Management Service can map it onto available compute resources and execute the steps in appropriate order.

Screenshots of package pegasus-wms
python3-nipype
Neuroimaging data analysis pipelines in Python3
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Nipype interfaces Python to other neuroimaging packages and creates an API for specifying a full analysis pipeline in Python. Currently, it has interfaces for SPM, FSL, AFNI, Freesurfer, but could be extended for other packages (such as lipsia).

Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
python3-wdlparse
Workflow Description Language (WDL) parser for Python
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A Python package that provides the generated Hermes and Antlr4 WDL parsers for Python.

snakemake
pythonic workflow management system
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Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific language (DSL) in Python style, together with a fast and comfortable execution environment.

Please cite: Johannes Köster and Sven Rahmann: Snakemake-a scalable bioinformatics workflow engine. Bioinformatics (2012)
Registry entries: Bio.tools  SciCrunch  Bioconda 
toil
cross-platform workflow engine
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Toil is a scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python. It works with several well established load balancers like Slurm or the Sun Grid Engine. Toil is also compatible with the Common Workflow Language (CWL) via the "toil-cwl-runner" interface, which this package make available via the Debian alternativess system under the alias "cwl-runner".

Please cite: John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten: Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology 35(4):314–316 (2017)
Registry entries: Bioconda 

Official Debian packages with lower relevance

cwlformat
code formatter for Common Workflow Language
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CWL Format is a specification and a reference implementation for a very opinionated CWL code formatter.

It outputs Common Workflow Language(CWL) in a standardized YAML format. It has no settings or options because you have better things to do with your time. And because CWL Format is always correct.

libbenchmark-tools
Microbenchmark support library, tools and documentation
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Library to support the benchmarking of functions, similar to unit-tests.

This package contains tools and documentation.

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