Debian Science Workflow packages

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.

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.

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.

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 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.

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 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.

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).

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

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.

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".

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.

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

This package contains tools and documentation.