Creating a New App Interface¶
Creating a New App Interface¶
Each app in the DE is built on one tool (executable or binary), but each tool can have more than one app interface. You can create your own app interface, or workflow based on a sequence of different apps, for the tool you want, right within the DE, using the WYSIWYG (What You See Is What You Get) interface. This interface allows you to drag and drop items into the interface.
If you’re new to this process, you may want to watch the YouTube video, Creating and Modifying Apps: Customizing your tools.
Step 1: Complete the steps for Dockerizing your tool for use in the DE¶
All tools are now Dockerized so they run faster and more efficiently in the DE. For instructions on how to do so, see Dockerizing Your Tools for the CyVerse Discovery Environment. For steps on creating a new tool or requesting installation of a new tool, see NEED
Step 2: Decide how you want to create the app and open the Create Apps window¶
Before you begin, you might want to search the list of available tools to see if the tool (executable or binary) you want to use for your app interface is available in the DE. If the tool or tool version you want to use is not listed, you must first request that the tool be installed.
The first step in creating a new app interface for an available tool is deciding which method you want to use to create the interface. There are three ways in which you can create an interface for a tool that is available for use in the DE:
- Copy and edit an existing app: This method is useful if you want to create a similar app based on the same tool or if you want to see how someone else created theirs.
- Edit an app in your Apps under development folder: Use this method to change settings for an app you created that is still in your Apps under development folder (because it has not yet been shared, you can still edit it). This is a useful way to create different variants of your app for different uses, as well as fine-tune or change settings and layout.
- Create a new app from scratch: This method allows you to create an app from the beginning with no preconceived notion.
- You also can “jump-start” your new app by clicking to select the tool name in the Manage Tools window.
To learn how to use each of these methods, see Creating, Copying, and Editing DE Apps.
Step 3: Select the tool¶
Select the tool and version to use and then enter the app’s name and description. For more information, see Selecting the Tool and Naming the App.
Step 4: Design the interface for your app¶
This is the meat and potatoes of creating the app interface. There are a number of different field types you can add to the interface. You can customize field names, specify the number and type of input files, add descriptive text, and much more. As you move through the process, it is a good idea to preview the app and test it out to make sure it’s doing what you want to do and looking how you want it to look. Remember to save frequently. Once saved, your app is available in your Apps under development workspace folder, where you can edit it at any time. For more information, see Designing the Interface.
Step 5: Test the app¶
Once you’ve finished designing and saved the app, it is immediately available in your Apps under development folder. From there, you can test it — see how it works, which fields are required, how it functions — and then edit it some more if you like and try it out on some analyses. In short, this is the time to put yourself in a new user’s shoes and make sure your app is useful to users and a good example of your work.
Remember: Once you’ve shared the app, you won’t be able to edit the app again; you can edit the user manual at any time. Now’s the time to make sure it really works and works well.
Need assistance?¶
If you have problems or need assistance, you can submit feedback right within the DE.
Creating a New App Interface Quick Start¶
Creating a New App Interface Quick Start¶
You can easily create a new interface for a DE app directly within the Discovery Environment. There are three ways in which you can create or edit an app for use in the Discovery Environment:
- Copy and edit an existing app: This method is useful if you want to create a similar app based on the same tool, if you want to see how someone else created their app, or if you just want to play with how to create or edit a tool interface.
- Create a new app interface from scratch: This method allows you to create an app interface from the beginning with no preconceived notion. This is the most frequently used method.
- Edit an app interface you created: Use this method to change settings in an app you created. This is a useful way to create different variants of your app for different uses, as well as to fine-tune or change settings and layout.
You can define the app’s arguments, settings, and layout. Once the app is to your satisfaction, it is immediately available in your DE personal workspace, where you can use it to run analyses, or share it with the user community.
The main steps to creating a new app are:
- Click Apps to open the Apps window.
- Select the method to use for creating the app – whether creating a new app from scratch, copying an existing app, or editing a public app.
- Search for the tool (executable or binary) to use for your app interface.
Tip
Tool not there? If the tool and version you want to use for your app interface is not in the list, you will need to request that it be installed.
- Enter basic information about your app.
- Specify the parameters (arguments) that define the functionality and appearance for your app.
- Preview the app and test your app to verify that it looks and functions the way you want it to.
- Save.
- Open the app in your Workspace Apps under development folder and test.
- If necessary, edit the app and preview again, repeating until the app is to your satisfaction, and then save.
- When you want to share it with other users, edit the documentation page for your app and then submit it for public use so other users can use your app for their analyses.
For more information on creating and editing DE apps, please see the related Table of Contents in the left pane.
Creating, Copying, and Editing DE Apps¶
Before you begin, you might want to search the list of available tools to see if the tool and version you want to use for your app interface is available in the DE. If it is not listed, you must first Dockerize the tool and then request that the tool be installed.
You can either create a new app from scratch, copy a public app, or edit an app in your Apps under Development folder (an app that you haven’t shared with the public yet). Most people jump right in by creating a new app.
If you don’t want to start from scratch, a useful tip is to copy an app in the Public Apps folder, then make any changes you want to that app–perhaps using a different version of the tool, or changing the name of a field–and then save to a new app name to make a totally new app.
You also can create a new workflow.
Main Steps¶
You may want to begin by reading Creating a New App Interface.
- Designing the Interface
- About the Create App window
- About designing the interface
- Next Steps
- Selecting the Tool and Naming the App
- Adding and Editing App Sections
- Adding and Deleting File and Folder Input Fields for Your App
- Adding List Fields to Your App
- Deleting a list field
- Adding Text, Integer, Checkbox, and Variable Input Fields to Your App
- Adding and Deleting Output Fields for Your App
- Adding an output field
- Deleting an output file or folder field
- Adding Reference Genome, Reference Sequence, and Reference Annotation fields
- Deleting a reference genome, sequence, or annotation field
- Moving fields in your app
- Setting the Argument Order
- Previewing the App and JSON
- Managing Tools in the DE
- Dockerizing Your Tools for the CyVerse Discovery Environment
- Background
- What is Docker?
- Using Docker in the CyVerse DE
- Steps for Dockerizing a tool in the DE
- Prerequisites
- Steps
- Step 1: Check if the tool and correct version are already installed in the DE.
- Step 2: Create the Dockerfile following best practices.
- Sample Dockerfile 1: hisat2
- Sample Dockerfile 2: NCBI SRA Submission pipeline
- Step 3: Build and test the Dockerized tool.
- Step 4: Request installation of the Dockerized tool.
- Step 5: Create and save the new app interface in the DE.
- Step 6: Test your app in the DE.
- Optional Steps
- Sharing (publishing) your app in the DE
- Editing an unshared app
- Deleting/editing a publicly shared app
- Requesting a different category for your app
- Examples of Dockerization of tools in the DE
- FAQs – Dockerizing
- Future enhancements
- Sharing your App or Workflow and Editing the User Manual
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