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
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Debian Science Workflow packages
Official Debian packages with high relevance
capsule-nextflow
packaging and deployment tool for Java applications
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Versions of package capsule-nextflow |
Release | Version | Architectures |
sid | 1.1.1+dfsg-1 | all |
trixie | 1.1.1+dfsg-1 | all |
bookworm | 1.1.1+dfsg-1 | all |
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License: DFSG free
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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.
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coop-computing-tools
cooperative computing tools
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Versions of package coop-computing-tools |
Release | Version | Architectures |
bullseye | 7.1.2-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 9.9-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 7.0.9-2 | amd64,arm64,armhf,i386 |
bookworm | 9.9-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 9.9-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 4.0-1.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package coop-computing-tools: |
uitoolkit | ncurses |
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License: DFSG free
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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.
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cwltool
Common Workflow Language reference implementation
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Versions of package cwltool |
Release | Version | Architectures |
bookworm | 3.1.20230209161050-1 | all |
stretch | 1.0.20170114120503-1 | all |
buster | 1.0.20181217162649+dfsg-10 | all |
bullseye | 3.0.20210124104916-3+deb11u1 | all |
trixie | 3.1.20240909164951-2 | all |
sid | 3.1.20240909164951-2 | all |
upstream | 3.1.20241007082533 |
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License: DFSG free
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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.
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gearman
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Versions of package gearman |
Release | Version | Architectures |
jessie | 1.0.6-5 | all |
buster-backports | 1.1.19.1+ds-2~bpo10+1 | all |
stretch | 1.0.6-9 | all |
buster | 1.1.18+ds-3 | all |
sid | 1.1.20+ds-1.2 | all |
trixie | 1.1.20+ds-1.2 | all |
bookworm | 1.1.20+ds-1 | all |
bullseye | 1.1.19.1+ds-2 | all |
upstream | 1.1.21 |
Debtags of package gearman: |
role | metapackage |
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License: DFSG free
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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.
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gearman-tools
Tools for the Gearman distributed job queue
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Versions of package gearman-tools |
Release | Version | Architectures |
bullseye | 1.1.19.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.20+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.20+ds-1.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.1.20+ds-1.2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 1.1.18+ds-3 | amd64,arm64,armhf,i386 |
stretch | 1.0.6-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.6-5 | amd64,armel,armhf,i386 |
buster-backports | 1.1.19.1+ds-2~bpo10+1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 1.1.21 |
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License: DFSG free
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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.
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make
utility for directing compilation
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Versions of package make |
Release | Version | Architectures |
jessie | 4.0-8.1 | amd64,armel,armhf,i386 |
stretch | 4.1-9.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.2.1-1.2 | amd64,arm64,armhf,i386 |
bullseye | 4.3-4.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 4.3-4.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 4.3-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 4.3-4.1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 4.4.1 |
Debtags of package make: |
devel | buildtools |
interface | commandline |
role | program |
scope | utility |
suite | gnu |
works-with | software:source |
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License: DFSG free
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GNU Make is a utility which controls the generation of executables
and other target files of a program from the program's source
files. It determines automatically which pieces of a large program
need to be (re)created, and issues the commands to (re)create
them. Make can be used to organize any task in which targets (files)
are to be automatically updated based on input files whenever the
corresponding input is newer --- it is not limited to building
computer programs. Indeed, Make is a general purpose dependency
solver.
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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Versions of package pegasus-wms |
Release | Version | Architectures |
stretch | 4.4.0+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 4.4.0+dfsg-8 | amd64,arm64,armhf,i386 |
jessie | 4.4.0+dfsg-4 | amd64,armel,armhf,i386 |
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License: DFSG free
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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.
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python3-nipype
Neuroimaging data analysis pipelines in Python3
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Versions of package python3-nipype |
Release | Version | Architectures |
sid | 1.8.6-3 | all |
bullseye | 1.6.0-2 | all |
bookworm | 1.8.5-3 | all |
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License: DFSG free
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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)
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python3-wdlparse
Workflow Description Language (WDL) parser for Python
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Versions of package python3-wdlparse |
Release | Version | Architectures |
bookworm | 0.1.0-3 | all |
bullseye | 0.1.0-2 | all |
sid | 0.1.0-3 | all |
trixie | 0.1.0-3 | all |
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License: DFSG free
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A Python package that provides the generated Hermes and Antlr4 WDL parsers for
Python.
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snakemake
pythonic workflow management system
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Versions of package snakemake |
Release | Version | Architectures |
buster | 5.4.0-1 | all |
sid | 7.32.4-6 | all |
stretch | 3.10.0-1 | all |
bookworm | 7.21.0-1 | all |
bullseye | 5.24.1-2 | all |
trixie | 7.32.4-6 | all |
upstream | 8.20.6 |
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License: DFSG free
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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.
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toil
cross-platform workflow engine
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Versions of package toil |
Release | Version | Architectures |
buster | 3.18.0-2 | all |
bookworm | 5.9.2-2+deb12u1 | all |
sid | 6.1.0-4 | all |
bullseye | 5.2.0-5 | all |
upstream | 7.0.0 |
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License: DFSG free
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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)
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Official Debian packages with lower relevance
cwlformat
code formatter for Common Workflow Language
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Versions of package cwlformat |
Release | Version | Architectures |
trixie | 2022.02.18-3 | all |
sid | 2022.02.18-3 | all |
bookworm | 2022.02.18-2 | all |
bullseye | 2021.01.05-1 | all |
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License: DFSG free
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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.
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libbenchmark-tools
Microbenchmark support library, tools and documentation
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Versions of package libbenchmark-tools |
Release | Version | Architectures |
stretch-backports | 1.3.0-1~bpo9+1 | all |
bookworm | 1.7.1-1 | all |
bullseye | 1.5.2-2 | all |
sid | 1.8.3-3 | all |
experimental | 1.8.4-1~exp1 | all |
trixie | 1.8.3-3 | all |
buster | 1.4.1-3 | all |
upstream | 1.9.0 |
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License: DFSG free
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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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