Academy Documentation
  • Usage of Academy Documentation
  • Getting Started
    • Background Information
    • For Apollo Users
    • For Titan Users
    • For Scientists
    • For HPC Users
    • For Experienced Users
  • Cloud Computing
    • General Information
    • Cloud Computing for Scientists
    • Cloud Computing for HPC Users
  • Overview of the Platform
    • Overview of the Platform User Interface
    • Tool Library and App Introduction
  • Billing Access and Orgs
    • Orgs and Account Management
    • Billing and Pricing
  • Cohort Browser
    • Apollo Introduction
    • Overview of the Cohort Browser
    • Combining Cohorts
    • Genomic Variant Browser
    • Somatic Variants
  • JSON
    • Introduction
    • JSON on the Platform
  • Command Line Interface (CLI)
    • Introduction to CLI
    • Advanced CLI
  • Building Applets
    • Introduction
    • Bash
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: samtools
      • Example 4: cnvkit
    • Python
      • Example 1: Word Count (wc)
      • Example 2: fastq_quality_trimmer
      • Example 3: cnvkit
  • Building Workflows
    • Native Workflows
    • WDL
      • Example 1: hello
      • Example 2: Word Count (wc)
      • Example 3: fastq_trimmer
      • Example 4: cnvkit
      • Example 5: workflow
    • Nextflow
      • Resources To Learn Nextflow
      • Overview of Nextflow
      • Nextflow Setup
      • Importing Nf-Core
      • Building Nextflow Applets
      • Error Strategies for Nextflow
      • Job Failures
      • Useful Information
  • Interactive Cloud Computing
    • Cloud Workstation
    • TTYD
    • TTYD vs Cloud Workstation
    • JupyterLab
      • Introduction
      • Running a JupyterLab Notebook
  • Docker
    • Using Docker
    • Creating Docker Snapshots
    • Running Docker with Swiss Army Knife
  • Portals
    • Overview of JSON files for Portals
    • Branding JSON File
    • Home JSON File
    • Navigation JSON File
    • Updating Your Portal
  • AI/ ML Accelerator
    • Data Profiler
      • Introduction to Data Profiler
      • Utilizing Data Profiler Navigator
      • Dataset Level Screen
      • Table Level Screen
      • Column Level Screen
      • Explorer Mode
      • Accessing Data Profiler in ML JupyterLab
    • ML JupyterLab
      • Introduction to ML JupyterLab
      • Getting Started in ML JupyterLab
      • In App Features
      • Getting Started with ML JupyterLab
    • MLflow
      • Introduction to MLflow
      • Getting Started with MLflow
      • Using MLflow Tracking Server
      • Model Registry
      • Using Existing Model
      • Utilizing MLflow in JupyterLab
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  1. Building Applets

Bash

In this section, we will build several native bash applets that will increase in complexity:

  1. An applet that takes an input files, runs a single Unix command, and returns the result as a file.

  2. An applet that includes a binary executable file in the resources directory.

  3. An applet that installs the dependency cnvkit at runtime and then as an asset.

  4. An applet that runs samtools.

In order to kill a job/ workflow/ app/applet you will need to terminate the job/ analysis. Please use dx terminate or terminate in the Monitor tab in the UI.

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Last updated 1 year ago

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