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It is also possible to port existing scripts and workflows to Nextflow. Supported scripting languages include bash, csh, ksh, Python, Ruby, and R. Any scripting language that uses the standard Unix shebang declaration (#!/bin/bash) is compatible with Nextflow. Below is an example of a workflow consisting of only one process:
A common value is /bin/sh, but some systems such as Solaris have the POSIX-compatible shell at /usr/xpg4/bin/sh. [13] In many Linux systems, /bin/sh is a hard or symbolic link to /bin/bash, the Bourne Again shell (BASH). Using bash-specific syntax while maintaining a shebang pointing to sh is also not portable. [14]
It is a container hypervisor providing an API to manage LXC containers. [14] The LXD project was started in 2015 and was sponsored from the start by Canonical Ltd. , the company behind Ubuntu . On 4 July 2023, the LinuxContainers project announced that Canonical had decided to take over the LXD project but a fork called Incus was made.
The main classes of Docker objects are images, containers, and services. [23] A Docker container is a standardized, encapsulated environment that runs applications. [26] A container is managed using the Docker API or CLI. [23] A Docker image is a read-only template used to build containers. Images are used to store and ship applications. [23] A ...
LXSS Manager Service is the service in charge of interacting with the subsystem (through the drivers lxss.sys and lxcore.sys), and the way that Bash.exe (not to be confused with the Shells provided by the Linux distributions) launches the processes, as well as handling the Linux system calls and the binary locks during their execution. [38]
Singularity is a free and open-source computer program that performs operating-system-level virtualization also known as containerization. [4]One of the main uses of Singularity is to bring containers and reproducibility to scientific computing and the high-performance computing (HPC) world.
Container Linux provides no package manager as a way for distributing payload applications, requiring instead all applications to run inside their containers. Serving as a single control host, a Container Linux instance uses the underlying operating-system-level virtualization features of the Linux kernel to create and configure multiple containers that perform as isolated Linux systems.
$ # bash shell $ /bin/bash-c 'echo a{p,c,d,b}e' ape ace ade abe $ # A traditional shell does not produce the same output $ /bin/sh-c 'echo a{p,c,d,b}e' a{p,c,d,b}e When brace expansion is combined with wildcards, the braces are expanded first, and then the resulting wildcards are substituted normally.