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

Coop-computing-tools
cooperative computing tools
Maintainer: Alastair McKinstry
Versions of package coop-computing-tools
ReleaseVersionArchitectures
wheezy3.5.1-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster7.0.9-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch4.0-1.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye7.1.2-5amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid7.2-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
Debtags of package coop-computing-tools:
uitoolkitncurses
Popcon: 6 users (5 upd.)*
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License: DFSG free
Git

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
Common Workflow Language reference implementation
Versions of package cwltool
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sid3.0.20210124104916-3all
stretch1.0.20170114120503-1all
buster1.0.20181217162649+dfsg-10all
bullseye3.0.20210124104916-3all
upstream3.1.20210628163208
Popcon: 14 users (15 upd.)*
Newer upstream!
License: DFSG free
Git

This is the reference implementation of the Common Workflow Language standards.

The CWL open standards are for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry.

The CWL reference implementation (cwltool) is intended to be feature complete and to provide comprehensive validation of CWL files as well as provide other tools related to working with CWL descriptions.

Please cite: Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić, Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes and Luka Stojanovic: Common Workflow Language, v1.0. (2016)
Registry entries: SciCrunch  OMICtools  Bioconda 
Gearman
Distributed job queue
Versions of package gearman
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jessie1.0.6-5all
buster1.1.18+ds-3all
squeeze0.13-1all
wheezy0.33-2all
sid1.1.19.1+ds-2all
stretch1.0.6-9all
bullseye1.1.19.1+ds-2all
Debtags of package gearman:
rolemetapackage
Popcon: 0 users (0 upd.)*
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License: DFSG free
Git

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
Versions of package gearman-tools
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wheezy0.33-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
buster1.1.18+ds-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
bullseye1.1.19.1+ds-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid1.1.19.1+ds-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
jessie1.0.6-5amd64,armel,armhf,i386
stretch1.0.6-9amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
squeeze0.13-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Popcon: 15 users (9 upd.)*
Versions and Archs
License: DFSG free
Git

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
コンパイルを制御するユーティリティ
Versions of package make
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bullseye4.3-4.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
sid4.3-4.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
squeeze3.81-8amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
jessie4.0-8.1amd64,armel,armhf,i386
wheezy3.81-8.2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch4.1-9.1amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster4.2.1-1.2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Debtags of package make:
develbuildtools
interfacecommandline
roleprogram
scopeutility
suitegnu
works-withsoftware:source
Popcon: 32980 users (5486 upd.)*
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License: DFSG free
Git

GNU Make は、プログラムのソースファイルからプログラムの実行ファイルやその他の 対象ファイルを生成する作業を制御するユーティリティです。大きなプログラムの どの部分を (再) 生成すべきかを自動判定し、その (再) 生成に必要なコマンドを 発行します。Make は入力ファイルに基づいて、対応する入力の更新に応じて対象 (ファイル) を更新する必要があるどんなタスクに対しても利用できます --- コンピュータプログラムのビルドに限りません。まさに、Make は汎用目的の 依存関係解決ユーティリティなのです。

The package is enhanced by the following packages: make-doc
Pegasus-wms
Scientific workflow management system for HTCondor
Versions of package pegasus-wms
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buster4.4.0+dfsg-8amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy4.0.1+dfsg-8amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc
jessie4.4.0+dfsg-4amd64,armel,armhf,i386
stretch4.4.0+dfsg-6amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
Popcon: 3 users (4 upd.)*
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License: DFSG free

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
Versions of package python3-nipype
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bullseye1.6.0-2all
sid1.6.0-2all
Popcon: 1 users (2 upd.)*
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License: DFSG free
Git

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
Versions of package python3-wdlparse
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bullseye0.1.0-2all
sid0.1.0-2all
Popcon: 0 users (4 upd.)*
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License: DFSG free
Git

A Python package that provides the generated Hermes and Antlr4 WDL parsers for Python.

Snakemake
pythonic workflow management system
Versions of package snakemake
ReleaseVersionArchitectures
sid5.24.1-2all
buster5.4.0-1all
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stretch3.10.0-1all
Popcon: 6 users (7 upd.)*
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License: DFSG free
Git

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  OMICtools  Bioconda 
Toil
cross-platform workflow engine
Versions of package toil
ReleaseVersionArchitectures
buster3.18.0-2all
sid5.2.0-5all
bullseye5.2.0-5all
Popcon: 3 users (8 upd.)*
Versions and Archs
License: DFSG free
Git

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: OMICtools  Bioconda 

Official Debian packages with lower relevance

Cwlformat
code formatter for Common Workflow Language
Versions of package cwlformat
ReleaseVersionArchitectures
sid2021.01.05-1all
bullseye2021.01.05-1all
Popcon: 1 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

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
Versions of package libbenchmark-tools
ReleaseVersionArchitectures
bullseye1.5.2-2all
buster1.4.1-3all
sid1.5.2-2all
upstream1.5.5
Popcon: 0 users (0 upd.)*
Newer upstream!
License: DFSG free
Git

Library to support the benchmarking of functions, similar to unit-tests.

This package contains tools and documentation.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 196754