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Revertfix
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mih authored Nov 15, 2023
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or checkout. This has advantages: The repository is leaner, it is easier
for administrators to perform garbage collections, and it is required if you
want to push to it at all times. You can find out more on what bare repositories are and how to use them
in the Git documentation at `git-scm.com/book/Git-on-the-Server-Getting-Git-on-a
-Server <https://git-scm.com/book/Git-on-the-Server-Getting-Git-on-a
`in the Git documentation <https://git-scm.com/book/en/v2/Git-on-the-Server-Getting-Git-on-a
-Server>`__.

bash
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Docker
`Docker <https://www.docker.com>`_ is a containerization software that can package software into :term:`software container`\s, similar to :term:`Singularity`.
Find out more on `wikipedia.org/wiki/Docker_(software) <https://en.wikipedia.org/wiki/Docker_(software)>`__.
Find out more on `Wikipedia <https://en.wikipedia.org/wiki/Docker_(software)>`__.

Docker-Hub
.. index::
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.. index:: ! operating system concept; environment variable

A variable made up of a name/value pair. Programs using a given environment variable will use its associated value for their execution.
You can find out a bit more :ref:`in the Find-out-more on environment variables <fom-envvar>`.
See the :ref:`Find-out-more on environment variables <fom-envvar>` for details.

ephemeral clone
.. index:: clone (ephemeral); DataLad concept
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Git
A version control system to track changes made to small-sized files over time. You can find out
more about Git in `the (free) GitPro book git-scm.com/book <https://git-scm.com/book/en/v2>`_
or `interactive Git tutorials try.github.io <https://try.github.io>`_ on :term:`GitHub`.
more about Git in `the (free) GitPro book <https://git-scm.com/book/en/v2>`_
or `interactive Git tutorials <https://try.github.io>`_ on :term:`GitHub`.

git-annex
A distributed file synchronization system, enabling sharing and synchronizing collections
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high-throughput computing
HTC
A computing environment build from a bond of computers and tuned to deliver large amounts of computational power to allow parallel processing of independent computational jobs. For more information, see `the Wikipedia entry at wikipedia.org/wiki/High-throughput_computing <https://en.wikipedia.org/wiki/High-throughput_computing>`_.
A computing environment build from a bond of computers and tuned to deliver large amounts of computational power to allow parallel processing of independent computational jobs. For more information, see `Wikipedia <https://en.wikipedia.org/wiki/High-throughput_computing>`_.

http
.. index:: protocol; http
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pipe
.. index:: ! operating system concept; pipe

Unix concept: A mechanism for providing the output of one command (:term:`stdout`) as the input of a next command (:term:`stdin`) in a Unix terminal. The standard syntax are multiple commands, separated by vertical bars (the "pipes", "|"). Read more `on Wikipedia at wikipedia.org/wiki/Pipeline_(Unix) <https://en.wikipedia.org/wiki/Pipeline_(Unix)>`_.
Unix concept: A mechanism for providing the output of one command (:term:`stdout`) as the input of a next command (:term:`stdin`) in a Unix terminal. The standard syntax are multiple commands, separated by vertical bars (the "pipes", "|"). Read more `on Wikipedia <https://en.wikipedia.org/wiki/Pipeline_(Unix)>`_.
provenance
A record that describes entities and processes that were involved in producing or influencing
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Git concept; Squashing is a Git operation which rewrites history by taking
a range of commits and squash them into a single commit. For more information
on rewriting Git history, checkout section :ref:`history` and the
`documentation at git-scm.com/book/en/v2/Git-Tools-Rewriting-History <https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History>`__.
`Git documentation <https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History>`__.

SSH
.. index:: concepts; SSH
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Singularity
`Singularity <https://sylabs.io/docs>`_ is a containerization software that can package software into :term:`software container`\s.
It is a useful alternative to :term:`Docker` as it can run on shared computational infrastructure.
Find out more on `Wikipedia at wikipedia.org/wiki/Singularity_(software) <https://en.wikipedia.org/wiki/Singularity_(software)>`__.
Find out more on `Wikipedia <https://en.wikipedia.org/wiki/Singularity_(software)>`__.

Singularity-Hub
`singularity-hub.org <https://singularity-hub.org>`_ was a Singularity container portal.
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You can get a short intro to the terminal and useful commands in the section :ref:`howto`.

Ubuntu
A common Linux distribution. `Find more information at ubuntu.com <https://ubuntu.com>`__.
A common Linux distribution. `More information here <https://ubuntu.com>`__.

UUID
Universally Unique Identifier. It is a character string used for *unambiguous*
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