.. DO NOT EDIT THIS FILE. This file is autogenerated from glossary_generator.py, update that instead. Dockstore Dictionary ==================== .. hlist:: :columns: 3 * :ref:`dict .dockstore.yml` * :ref:`dict absolute path` * :ref:`dict AGC` * :ref:`dict Amazon Genomics CLI` * :ref:`dict AnVIL Project` * :ref:`dict API` * :ref:`dict AWS` * :ref:`dict BD Catalyst` * :ref:`dict BDC` * :ref:`dict BioData Catalyst` * :ref:`dict Cancer Genomics Cloud` * :ref:`dict categories` * :ref:`dict CGC` * :ref:`dict CLI` * :ref:`dict cloud computing` * :ref:`dict collection` * :ref:`dict Common Workflow Language` * :ref:`dict container` * :ref:`dict Cromwell` * :ref:`dict CWL` * :ref:`dict cwltool` * :ref:`dict DAG` * :ref:`dict descriptor file` * :ref:`dict Docker` * :ref:`dict Docker container` * :ref:`dict Docker image` * :ref:`dict Dockerfile` * :ref:`dict Dockstore CLI` * :ref:`dict Dockstore GitHub App` * :ref:`dict DOI` * :ref:`dict DRS` * :ref:`dict DS-I Africa` * :ref:`dict EC2` * :ref:`dict egress` * :ref:`dict eLwazi` * :ref:`dict entry` * :ref:`dict environment variable` * :ref:`dict faceted search` * :ref:`dict FAIR` * :ref:`dict GA4GH` * :ref:`dict Galaxy` * :ref:`dict Galaxy workflow` * :ref:`dict GCP` * :ref:`dict Gen3` * :ref:`dict GitHub App registration` * :ref:`dict GitHub App tool` * :ref:`dict GitHub App workflow` * :ref:`dict immutable` * :ref:`dict interoperable` * :ref:`dict JSON` * :ref:`dict Jupyter` * :ref:`dict kernel` * :ref:`dict Kids First` * :ref:`dict labels` * :ref:`dict launch with` * :ref:`dict layer` * :ref:`dict legacy registration` * :ref:`dict legacy tool` * :ref:`dict legacy workflow` * :ref:`dict miniwdl` * :ref:`dict NCI` * :ref:`dict NCPI` * :ref:`dict Nextflow` * :ref:`dict NFL` * :ref:`dict NHGRI` * :ref:`dict NHLBI` * :ref:`dict NIH` * :ref:`dict notebook` * :ref:`dict OICR` * :ref:`dict ORCID` * :ref:`dict organization` * :ref:`dict parameter file` * :ref:`dict parent image` * :ref:`dict preemptible` * :ref:`dict primary descriptor file` * :ref:`dict secondary descriptor file` * :ref:`dict Seven Bridges` * :ref:`dict Spot Instance` * :ref:`dict Task Execution Service` * :ref:`dict Terra` * :ref:`dict TES` * :ref:`dict tool` * :ref:`dict topic` * :ref:`dict TRS` * :ref:`dict UCSC` * :ref:`dict VM` * :ref:`dict WDL` * :ref:`dict WES` * :ref:`dict workflow` * :ref:`dict Workflow Description Language` * :ref:`dict Workflow Execution Service` * :ref:`dict YAML` .. _dict .dockstore.yml: .dockstore.yml -------------- This file is part of :ref:`dict GitHub App registration`. It indexes workflows or tools within a repository, including their optional test parameter files, and the author(s) of said workflows or tools. Further reading: :doc:`/assets/templates/template ` .. _dict absolute path: absolute path ------------- A path that starts with the character ``/`` and contains the full set of directories necessary to resolve a file, starting from the root directory of the repository or filesystem. For example: ``/Dockstore.cwl`` or ``/bin/sh`` .. _dict AGC: AGC --- *abbreviation for* :ref:`dict Amazon Genomics CLI` .. _dict Amazon Genomics CLI: Amazon Genomics CLI ------------------- A :ref:`dict CLI`-based tool that supports launching bioinformatics-related workflows on :ref:`dict AWS` cloud infrastructure. The :ref:`dict Dockstore CLI` can launch workflows on AWS using Amazon Genomics CLI's :ref:`dict WES` implementation. see also :ref:`dict AGC` Further reading: ``_ .. _dict AnVIL Project: AnVIL Project ------------- *abbreviation for* Analysis Visualization and Informatics Labspace A federated cloud platform funded by :ref:`dict NHGRI` designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. Sometimes referred to as just "the AnVIL" or "AnVIL". Further reading: ``_ .. _dict API: API --- *abbreviation for* Application Programmer Interface A software connection or interface used to exchange data, often between two different platforms. Communication between different cloud platforms is mediated by various APIs, such as :ref:`dict TES`. .. _dict AWS: AWS --- *abbreviation for* Amazon Web Services A provider of cloud services, most notably cloud computing and cloud storage, available on-demand and hosted by Amazon. Netflix and AirBnB are examples of a system that is powered by AWS. Some bioinformatics systems such as :ref:`dict Seven Bridges` can leverage AWS by launching workflows on :ref:`dict EC2` instances. see also :ref:`dict GCP` Further reading: ``_ .. _dict BD Catalyst: BD Catalyst ----------- *abbreviation for* :ref:`dict BioData Catalyst` .. _dict BDC: BDC --- [pronounced "bee-dee-see"] *abbreviation for* :ref:`dict BioData Catalyst` .. _dict BioData Catalyst: BioData Catalyst ---------------- A cloud-based platform funded by :ref:`dict NHLBI` to provide tools, applications, and workflows in secure workspaces to expand research in heart, lung, blood, and sleep health. Further reading: ``_ .. _dict Cancer Genomics Cloud: Cancer Genomics Cloud --------------------- A cloud platform by :ref:`dict Seven Bridges` and funded by :ref:`dict NCI` for bioinformatics analysis. .. _dict categories: categories ---------- A group of workflows or tools curated by Dockstore with a similar scientific purpose. .. _dict CGC: CGC --- *abbreviation for* :ref:`dict Cancer Genomics Cloud` .. _dict CLI: CLI --- *abbreviation for* Command Line Interface A program that can be interacted with on the command line, usually via "Terminal" on MacOS and Linux or "cmd"/Command Prompt on Windows. CLI programs generally do not have a graphical user interface. Further reading: ``_ .. _dict cloud computing: cloud computing --------------- Doing computational tasks on a remote machine that is made available on-demand without the user having to manage all aspects of it. Generally implies that the user is essentially renting computational resources from someone else. Well-known cloud providers include :ref:`dict GCP`, :ref:`dict AWS`, Microsoft Azure, and Alibaba Cloud. Further reading: ``_ .. _dict collection: collection ---------- A group of at least one :ref:`dict entry` on Dockstore that the members of an :ref:`dict organization` found useful, created themselves, or considered interesting. Each collection has a description, which you can read to see why the organization compiled workflows/tools in a collection .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict Common Workflow Language: Common Workflow Language ------------------------ A workflow language that describes how to run command-line tools. :ref:`dict WDL` and CWL are relatively similar in principle, and code written in one language can often be translated into the other with some workarounds, but they are two different standards and each have unique features. For example, CWL has the ability to use Javascript expressions within its own commands. CWL makes a distinction between a :ref:`dict tool` and a :ref:`dict workflow`. see also :ref:`dict CWL`, :ref:`dict WDL` Further reading: ``_ .. _dict container: container --------- An emulated computer system that contains programs and their prerequisites, but does not contain the entire operating system. Unlike a :ref:`dict VM`, a container shares the same kernel as the host OS. A well known type of container is a :ref:`dict Docker container`. Further reading: ``_ .. _dict Cromwell: Cromwell -------- An open-source :ref:`dict WDL` executor managed by the Broad Institute. Cromwell is the default :ref:`dict WDL` executor for the :ref:`dict Dockstore CLI` and is the executor used by :ref:`dict Terra`. .. note:: This term as we define it here is associated with Broad Institute and may have different definitions in other contexts. see also :ref:`dict miniwdl` Further reading: ``_ .. _dict CWL: CWL --- *abbreviation for* :ref:`dict Common Workflow Language` .. _dict cwltool: cwltool ------- An open-source :ref:`dict CWL` executor which serves as the official reference implementation of :ref:`dict Common Workflow Language`. It is used by the :ref:`dict Dockstore CLI` to run CWL tools and workflows. Further reading: ``_ .. _dict DAG: DAG --- *abbreviation for* Directed Acyclic Graph A directional graph like a flowchart that does not have any loops. On Dockstore we use DAGs to show the steps that a workflow takes. Further reading: ``_ .. _dict descriptor file: descriptor file --------------- A file used to programmatically describe a tool or workflow. This file represents the instructions that will actually be executed. On Dockstore, we support .ga, .cwl, .wdl, and .nfl file extensions for :ref:`dict Galaxy`, :ref:`dict CWL`, :ref:`dict WDL`, and :ref:`dict Nextflow` respectively. .. _dict Docker: Docker ------ [pronounced "daw-ker", rhymes with walker] A program that can create "images" which are somewhat similar to virtual machines, as well as run those images. In the context of bioinformatics, this technology has two main benefits: First, a :ref:`dict Docker image` bundles up everything a given piece of software needs to run, meaning that someone who wants to run (for example) samtools via Docker only needs to install Docker, not samtools. Second, an instance of a Docker image is a relatively standardized environment even when running on different backends, meaning that two people running the same software in the same Docker image on two different computers are likely to get the exact same results. In other words, Docker is good for reproducibility and ease of use. Further reading: ``_ .. _dict Docker container: Docker container ---------------- In order to actually use the software inside a :ref:`dict Docker image` using the `docker run` command, the Docker program creates a writable :ref:`dict layer` on top of the image, which leads to the creation of a :ref:`dict Docker container`. You can think of a Docker image as an unchanging template, and a Docker container as a writable instance generated from that template. A Docker image can exist on its own, but a Docker container requires a Docker image. Further reading: ``_ .. _dict Docker image: Docker image ------------ A read-only file that represents a filesystem that contains some sort of code and that code's dependencies. A Docker image can be created using the `docker build` command in conjunction with a :ref:`dict Dockerfile`. If a workflow language references a Docker image, then the workflow executor will download that Docker image (unless was already downloaded previously) and add a writable layer onto the Docker image, which results in the creation of a :ref:`dict Docker container`. .. _dict Dockerfile: Dockerfile ---------- A file describing the creation of a :ref:`dict Docker image` by running commands that each form a :ref:`dict layer`. Further reading: ``_ .. _dict Dockstore CLI: Dockstore CLI ------------- *abbreviation for* Dockstore Command Line Interface A command-line program developed by Dockstore. It is not required to use Dockstore, but it has many features to make running and developing workflows easier. see also :ref:`dict CLI` Further reading: :doc:`/advanced-topics/dockstore-cli/dockstore-cli-faq ` .. _dict Dockstore GitHub App: Dockstore GitHub App -------------------- The GitHub App that allows for Dockstore to automatically sync changes made in a GitHub repository with an :ref:`dict entry` in Dockstore. see also :ref:`dict GitHub App registration` Further reading: :doc:`/getting-started/github-apps/github-apps-landing-page ` .. _dict DOI: DOI --- *abbreviation for* Digital Object Identifier An identifier that provides a long-lasting link to some sort of :ref:`dict immutable` digital object. On Dockstore, you can use Zenodo to mint a DOI of your workflows and tools to increase reproducibility. .. _dict DRS: DRS --- [pronounced "derse", rhymes with verse] *abbreviation for* Data Repository Service A standardized :ref:`dict API`, created by the :ref:`dict GA4GH` Cloud Work Stream, that provides portable access to repositories of data resources. .. note:: This term as we define it here is associated with GA4GH and may have different definitions in other contexts. Further reading: ``_ .. _dict DS-I Africa: DS-I Africa ----------- *abbreviation for* Data Science for health discovery and Innovation in Africa An :ref:`dict NIH` initiative to leverage data science to address the African continent's public health needs. Further reading: ``_ .. _dict EC2: EC2 --- *abbreviation for* Elastic Compute Cloud The cloud computing side of :ref:`dict AWS`. You can make use of Amazon's :ref:`dict spot instance` feature, which may reduce the cost of running workflows, when using EC2 instances. Further reading: ``_ .. _dict egress: egress ------ [pronounced "ee-gress", rhymes with aggress] The action of leaving a place. In the context of :ref:`dict cloud computing`, data egress refers to data being moved from one location to another, such as from the cloud to a local machine, between cloud providers, and between locations of a single cloud provider. Data egress often results in the charge of fees (usually called egress charges). Data egress can be one of the most expensive cloud costs incurred. Sometimes, the person hosting the file is charged for data egress. Other times, the person downloading the file is charged (such as when downloading files from a Google bucket that has the requester-pays option enabled). .. note:: This term as we define it here is associated with cloud computing and may have different definitions in other contexts. .. _dict eLwazi: eLwazi ------ [pronounced "el-woz-ee", derived from the Xhosa word for knowledge (uLwazi) and the Luganda word for rock symbolizing robustness (Olwazi)] An African-lead open data science platform funded as part of the :ref:`dict NIH`'s :ref:`dict DS-I Africa` program. Further reading: ``_ .. _dict entry: entry ----- Shorthand for a :ref:`dict tool`, :ref:`dict workflow`, :ref:`dict notebook`, or service that has been registered on Dockstore. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict environment variable: environment variable -------------------- A variable that affects how processes run on a computer. For example, :ref:`dict cwltool` references the environment variable $TMPDIR when deciding where to place files. Further reading: ``_ .. _dict faceted search: faceted search -------------- A type of search which allows users to narrow down their results based upon certain aspects of the things being searched. On Dockstore, our faceted search at allows users to narrow down their search to a particular workflow language, author, and/or other fields. Further reading: ``_ .. _dict FAIR: FAIR ---- [pronounced "fair", rhymes with pear] *abbreviation for* Findable, Accessible, Interoperable, and Reusable A set of guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets. This concept is often applied to data, but can be applied to other assets such as workflows. Further reading: ``_ .. _dict GA4GH: GA4GH ----- *abbreviation for* Global Alliance For Genomics and Health A network of public and private institutions which aims to accelerate progress in genomic research and human health by cultivating a common framework of standards and harmonized approaches for effective and responsible genomic and health-related data sharing. Further reading: ``_ .. _dict Galaxy: Galaxy ------ An open-source platform that uses :ref:`dict FAIR` principles, most well-known for its web-based UI used to create and run a variety of bioinformatics tools. A Galaxy `instance` is a running Galaxy interface/server that can be used to create and execute tools and workflows. Further reading: ``_ .. _dict Galaxy workflow: Galaxy workflow --------------- A type of :ref:`dict workflow` that follows the standards of the :ref:`dict Galaxy` execution system. Dockstore supports the registration of Galaxy workflows with the file extension .ga Further reading: ``_ .. _dict GCP: GCP --- *abbreviation for* Google Cloud Platform A system used for cloud computing and cloud storage hosted by Google. Well-known users of GCP include LinkedIn and Verizon, but GCP can also power bioinformatics. :ref:`dict Terra` is an example of a bioinformatics system that runs on a GCP backend. When running workflows on GCP backends, make sure to account for the storage needed for your workflow, as GCP compute backends do not automatically scale their storage size at runtime. GCP backends allow you to make use of Google's :ref:`dict preemptible` feature, which may reduce the cost of running workflows. see also :ref:`dict EC2` Further reading: ``_ .. _dict Gen3: Gen3 ---- A data science platform affiliated with the University of Chicago. Hosts phenotypic and genotypic data for the :ref:`dict BD Catalyst`, :ref:`dict AnVIL Project`, :ref:`dict Kids First`, and :ref:`dict eLwazi` grants. Further reading: ``_ .. _dict GitHub App registration: GitHub App registration ----------------------- The recommended way to register a :ref:`dict tool` or :ref:`dict workflow` on Dockstore. This involves creating a :ref:`dict .dockstore.yml` file on the GitHub repository (other source-control methods are not supported) that hosts the tool or workflow, as well as installing the :ref:`dict Dockstore GitHub App`. This allows a Dockstore entry to remain in sync with the source-control repository automatically, including new branches, tagged commits, and releases created on GitHub after registration of the entry. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. Further reading: :doc:`/getting-started/github-apps/github-apps-landing-page ` .. _dict GitHub App tool: GitHub App tool --------------- A :ref:`dict tool` registered using the :ref:`dict Dockstore GitHub App`. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. see also :ref:`dict GitHub App registration` .. _dict GitHub App workflow: GitHub App workflow ------------------- A :ref:`dict workflow` registered with the :ref:`dict Dockstore GitHub App`. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. see also :ref:`dict GitHub App registration` .. _dict immutable: immutable --------- Unchanging, unable to be modified. Immutability implies that an object cannot be updated. .. _dict interoperable: interoperable ------------- The ability of data or tools from multiple resources to effectively integrate data, or operate processes, across all systems with a moderate degree of effort. .. _dict JSON: JSON ---- [pronounced "jason"] *abbreviation for* JavaScript Object Notation A human-readable file format that originated in JavaScript, but is now used by a variety of applications. Dockstore supports the inclusion of JSON and :ref:`dict YAML` files in entries to provide sample inputs for workflow and tool entries. Some workflow executors, such as :ref:`dict Cromwell`, can use these files to configure their inputs rather than having to manually listing every input when calling the workflow on the command line. see also :ref:`dict YAML` Further reading: ``_ .. _dict Jupyter: Jupyter ------- [pronounced "Jupiter" like the planet] A project focused on developing "notebooks" for programming languages, most famously Python due to it starting as a splinter of iPython in the early 2010s. Other languages such as R are also supported. Jupyter notebooks allow for blocks of code to be nestled between markdown text, allowing for easy documentation of the code blocks and reproducibility of analysis. Further reading: ``_ .. _dict kernel: kernel ------ An operating system's core program that is always loaded in memory, and modulates interactions between software and physical hardware, including but not limited to managing memory access for any program currently in RAM. Further reading: ``_ .. _dict Kids First: Kids First ---------- *abbreviation for* Gabriella Miller Kids First Program An :ref:`dict NIH` program, supported by the NIH Common Fund, relating to the influence of genomics on pediatric health, with a focus on pediatric cancer and structural birth abnormalities (such as cleft palate). Further reading: ``_ .. _dict labels: labels ------ On Dockstore, we use labels to "tag" Dockstore entries with information about them. Workflow or tool developers can add labels to a Dockstore :ref:`dict entry` page that they have edit access to. An entry's labels will appear in search results. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict launch with: launch with ----------- On Dockstore, this refers to the functionality of exporting a :ref:`dict workflow` to one of our cloud execution partners. .. _dict layer: layer ----- In the context of Docker, a layer is a component of a Docker image. Each `RUN`, `COPY`, and `ADD` instruction in a :ref:`dict Dockerfile` will lead to the creation of a layer. Further reading: ``_ .. _dict legacy registration: legacy registration ------------------- One of the two main ways of registering a :ref:`dict tool` or :ref:`dict workflow`. Legacy methods support a variety of source-control repositories, but new changes to the tool or workflow after registration will not be reflected on Dockstore until the maintainer of the Dockstore :ref:`dict entry` manually refreshes the tool or workflow in Dockstore's UI. For this reason, we generally recommend people use :ref:`dict GitHub App registration` instead. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict legacy tool: legacy tool ----------- On Dockstore, we use this term to refer to a :ref:`dict tool` that is registered using a :ref:`dict legacy registration` method. Legacy tools are not automatically synchronized with their source control repository, but can be updated manually by the tool maintainer. Additionally, legacy tools require a :ref:`dict Dockerfile` to be registered, and are versioned based on the tags of their associated :ref:`dict Docker image`. A legacy tool can be converted into a :ref:`dict GitHub App tool` via :doc:`the method described here `. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict legacy workflow: legacy workflow --------------- On Dockstore, we use this term to refer to a :ref:`dict workflow` that is registered using a :ref:`dict legacy registration` method. Legacy workflows are not automatically synchronized with their source control repository, but can be updated manually by the workflow maintainer. A legacy workflow can be converted into a :ref:`dict GitHub App workflow` via :doc:`the method described here `. .. note:: This term as we define it here is associated with Dockstore and may have different definitions in other contexts. .. _dict miniwdl: miniwdl ------- A Python-based :ref:`dict WDL` executor managed by the Chan Zuckerberg Initiative. .. note:: This term as we define it here is associated with Chan Zuckerberg Initiative and may have different definitions in other contexts. see also :ref:`dict Cromwell` Further reading: ``_ .. _dict NCI: NCI --- *abbreviation for* National Cancer Institute A division of the :ref:`dict NIH` focused on cancer research. .. note:: This term as we define it here is associated with NIH and may have different definitions in other contexts. Further reading: ``_ .. _dict NCPI: NCPI ---- *abbreviation for* NIH Cloud Platform Interoperability An effort to connect five :ref:`dict NIH` cloud projects and ensure they are interoperable. The five projects covered under this are the :ref:`dict AnVIL Project`, :ref:`dict BioData Catalyst`, Cancer Research Data Commons, :ref:`dict Kids First`, and the National Center for Biotechnology Information. .. note:: This term as we define it here is associated with NIH and may have different definitions in other contexts. Further reading: ``_ .. _dict Nextflow: Nextflow -------- A Java-based computational workflow engine. Dockstore supports the hosting of Nextflow workflows. Further reading: ``_ .. _dict NFL: NFL --- *abbreviation for* :ref:`dict Nextflow` An uncommon acronym for :ref:`dict Nextflow`. This abbreviation is not used as frequently as :ref:`dict CWL` or :ref:`dict WDL`, but does see usage occasionally. .. _dict NHGRI: NHGRI ----- *abbreviation for* National Human Genome Research Institute A division of the :ref:`dict NIH` that focus on genomics research. Funds the :ref:`dict AnVIL Project`. .. note:: This term as we define it here is associated with NIH and may have different definitions in other contexts. Further reading: ``_ .. _dict NHLBI: NHLBI ----- *abbreviation for* National Heart, Lungs, and Blood Institute A division of the :ref:`dict NIH` that focuses on heart, lung, blood, and sleep health. Funds the :ref:`dict BioData Catalyst` platform. .. note:: This term as we define it here is associated with NIH and may have different definitions in other contexts. Further reading: ``_ .. _dict NIH: NIH --- *abbreviation for* National Institutes of Health An American government institution, part of the Department of Health and Human Services (HHS), that engages in medical research. Further reading: ``_ .. _dict notebook: notebook -------- An interactive document, made up of "cells" containing code, text, and images, authored and executed in a browser-based programming environment. Project :ref:`dict Jupyter` popularized Python-based notebooks and maintains related specifications and software. Further reading: :doc:`/getting-started/getting-started-with-notebooks ` .. _dict OICR: OICR ---- *abbreviation for* Ontario Institute for Cancer Research A non-profit research institute based in Toronto that is focused on cancer detection and treatment. One of the two institutes involved in the development of Dockstore, the other being :ref:`dict UCSC`. Further reading: ``_ .. _dict ORCID: ORCID ----- [pronounced "or-kid", rhymes with kid] *abbreviation for* Open Researcher and Contributor ID A unique ID used to identify researchers and their work in a way that doesn't solely rely on names. Further reading: ``_ .. _dict organization: organization ------------ In the context of Dockstore, an organization is a representation of some sort of institute, grant, project, or company. Organizations are approved by Dockstore admins, but any user with at least two external accounts linked to their Dockstore account (and have the authority to speak for the institute, grant, etc. in a technical manner) can request the creation of an organization on Dockstore. Further reading: ``_ .. _dict parameter file: parameter file -------------- A :ref:`dict JSON` or :ref:`dict YAML` file that describes the inputs to a workflow, such as runtime parameters or links to cloud data. .. _dict parent image: parent image ------------ A :ref:`dict Docker image` which acts as the base upon which another Docker image is built. For example, including ``FROM ubuntu:22.04`` in a :ref:`dict Dockerfile` means that the resulting image will include everything inside ubuntu:22.04, plus any changes made by other commands in the Dockerfile. Parent images are sometimes called base images, but strictly speaking a base image is different (see further reading). Further reading: ``_ .. _dict preemptible: preemptible ----------- A type of :ref:`dict GCP` :ref:`dict VM` which may have its running jobs interrupted at any given time, and will be shut down if running for more than 24 hours. A preemptible machine is significantly cheaper than a standard VM, at the cost of possibly stopping before your computational work is finished. You can use preemptible machines when running workflows on GCP backends to save on compute costs. .. note:: This term as we define it here is associated with Google and may have different definitions in other contexts. see also :ref:`dict spot instance` Further reading: ``_ .. _dict primary descriptor file: primary descriptor file ----------------------- The :ref:`dict descriptor file` that provides the overall description of a workflow or tool, which Dockstore processes first when the workflow or tool is registered. .. _dict secondary descriptor file: secondary descriptor file ------------------------- An ancillary :ref:`dict descriptor file`, referenced by the :ref:`dict primary descriptor file` or another secondary descriptor file, that describes part of a workflow or tool. .. _dict Seven Bridges: Seven Bridges ------------- A cloud-based workflow execution platform developed by Seven Bridges Genomics. Seven Bridges supports the execution of :ref:`dict CWL` workflows and features a graph-based GUI to make workflow development easier. The computational backend of a Seven Bridges workspace can be selected by the user, with both :ref:`dict GCP` and :ref:`dict AWS` being supported. Dockstore supports directly importing :ref:`dict CWL` workflows into a Seven Bridges workspace. Seven Bridges is part of the :ref:`dict BioData Catalyst` consortium. see also :ref:`dict Terra` Further reading: ``_ .. _dict Spot Instance: Spot Instance ------------- A type of :ref:`dict EC2` instance which is usually much cheaper than the typical on-demand EC2 cost. A spot instance is not guaranteed to be available at any given time, as it is based upon currently unused EC2 availability. .. note:: This term as we define it here is associated with Amazon and may have different definitions in other contexts. see also :ref:`dict preemptible` Further reading: ``_ .. _dict Task Execution Service: Task Execution Service ---------------------- A standardized :ref:`dict API` developed by :ref:`dict GA4GH` for describing and executing batch execution tasks. Further reading: ``_ .. _dict Terra: Terra ----- A cloud-based workflow execution platform developed by the Broad Institute. Terra supports the execution of :ref:`dict WDL` workflows, Jupyter/R notebooks, and integrated apps. The computational backend of a Terra workspace is based upon Google, allowing Google-specific features such as :ref:`dict preemptible` machines to be used in workflows. Dockstore supports directly importing :ref:`dict WDL` workflows into a Terra workspace. Terra is part of the :ref:`dict BioData Catalyst`, :ref:`dict AnVIL Project`, and :ref:`dict eLwazi` consortia. see also :ref:`dict Seven Bridges` Further reading: ``_ .. _dict TES: TES --- *abbreviation for* :ref:`dict Task Execution Service` .. _dict tool: tool ---- A single command line program wrapped in a descriptor language. Languages that formally describe tools (such as :ref:`dict CWL`) may chain them together into a :ref:`dict workflow`. see also :ref:`dict workflow` Further reading: :doc:`/getting-started/intro-to-dockstore-tools-and-workflows ` .. _dict topic: topic ----- A short text description of an :ref:`dict entry`, :ref:`dict collection`, or :ref:`dict organization`. You can specify an entry's topic in :ref:`dict .dockstore.yml`. .. _dict TRS: TRS --- [pronounced "terse", rhymes with verse] *abbreviation for* Tool Registry Service A standardized :ref:`dict API`, created by the :ref:`dict GA4GH` Cloud Work Stream, that provides portable access to a registry of tools, workflows, and associated files. Every resource in a TRS registry has a public ID that can be used to retrieve it. Dockstore `provides `__ a TRS interface. .. note:: This term as we define it here is associated with GA4GH and may have different definitions in other contexts. Further reading: ``_ .. _dict UCSC: UCSC ---- *abbreviation for* University of California, Santa Cruz A public university located in Santa Cruz that is focused on undergraduate and graduate education and research. The Genomics Institute, a branch of UCSC's engineering department, is one of the two institutes involved in the development of Dockstore, the other being :ref:`dict OICR`. Further reading: ``_ .. _dict VM: VM -- *abbreviation for* virtual machine An emulated computer system that runs on another computer system. Usually implies that an entire operating system(s) (the guest OS) is being run on top of another operating system (the host OS) via the host's hypervisor. The hypervisor manages the execution of processes of the guest operating system. This is in contrast to a :ref:`dict container`, which do not involve hypervisors nor run entire guest operating systems. see also :ref:`dict container` .. _dict WDL: WDL --- [pronounced "widdle", rhymes with riddle] *abbreviation for* :ref:`dict Workflow Description Language` .. _dict WES: WES --- [pronounced "wes", rhymes with mess] *abbreviation for* :ref:`dict Workflow Execution Service` .. _dict workflow: workflow -------- A command line program wrapped in a descriptor language, which usually has multiple steps. In :ref:`dict CWL`, a workflow is usually made up of multiple tools. Other languages consider a workflow to be the basic unit. see also :ref:`dict tool` Further reading: :doc:`/getting-started/intro-to-dockstore-tools-and-workflows ` .. _dict Workflow Description Language: Workflow Description Language ----------------------------- A workflow language managed by the Open WDL Project that is designed to describe command line tools. Usually written as :ref:`dict WDL`. WDL and :ref:`dict CWL` are relatively similar in principle, and code written in one language can often be translated into the other with some workarounds, but they are two different standards and each have unique features. Unlike CWL, WDL does not have an official reference implementation, but :ref:`dict Cromwell` and :ref:`dict miniwdl` are popular implementations. see also :ref:`dict WDL`, :ref:`dict CWL` Further reading: ``_ .. _dict Workflow Execution Service: Workflow Execution Service -------------------------- A standardized :ref:`dict API` developed by :ref:`dict GA4GH` for describing a standard programmatic way to run and manage workflows. This standard, also known as :ref:`dict WES`, can be launched using the :ref:`dict Dockstore CLI` as described in this Dockstore blog post: Further reading: ``_ .. _dict YAML: YAML ---- [pronounced "yah-mul", rhymes with camel] *abbreviation for* YAML Ain't Markup Language Human-readable data-serialization language. Commonly used for configuration files. see also :ref:`dict JSON` Further reading: ``_