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.

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.

Gearman은 다른 컴퓨터로 작업을 내보내고, 작업에 더 적합한 컴퓨터로 함수 호출을 보내고, 병렬로 작업을 수행하고, 많은 함수 호출을 로드 밸런싱하거나, 또는 언어 사이에 함수를 호출하기 위한 시스템입니다.

이 패키지는 클라이언트와 서버 양쪽에 의존하는 빈 패키지입니다.

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 Make는 프로그램의 소스 파일에서 실행 및 다른 타켓 파일 생성을 제어하는 유틸리티입니다. Make는 생성 및 재생성이 필요한 거대한 프로그램의 일부를 자 동으로 결정하며, 그리고 생성 및 재생성에 필요한 명령어를 만듭니다. Make는 해당 입력이 최신이 될 때마다 입력 파일에 기반하여 타켓 (파일)이 자동으로 업 데이트 될 수 있도록 임의 태스크를 구성하는데 사용될 수 있습니다 -- Make는 컴퓨터 프로그램 구축에만 한정되지 않습니다. 실제로 Make는 범용의 의존성 해 결자 역활을 합니다.

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.