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Discovery Environment 2.0 Platform Guide

Goal

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Logging into the Discovery Environment (DE)

The Discovery Environment (DE) was designed to be an all-purpose bioinformatics workbench – tailored to the needs of scientists who have data to analyze but who may not have command line expertise. For example, many popular bioinformatics analyses and workflows (such as genome assembly, RNA-Seq, phylogeny methods, and GWAS) can be done from start to finish within the DE.

Some things to remember about the DE

  • Your analyses are not limited by your computer. All computation in the DE runs on CyVerse resources, enabling you to connect from your laptop or phone and launch jobs large and small.
  • Once you launch a job, it will run until completion. You can logout once a job is launched; you will get an automated email notification when the job completes.

Logging In

When you first navigate to the DE, you’ll be presented with the Dashboard view. This view contains links to news and videos related to CyVerse, along with a list of recently added applications that can be used to perform computational analyses. We welcome you to explore this information as much as you like, but you must log in before you can perform any tasks.

You may log in by clicking the profile icon in the upper right-hand corner of the DE, or by clicking SIGN IN when you encounter a message such as this one:

DE Login Required

After entering your username and password, you’ll be directed back to the view that you were previously on. For example, if you were on the Apps view then clicked SIGN IN, then you’ll return to the Apps view after entering your credentials. If you don’t have an account yet or you’ve forgotten your password, you can visit the CyVerse User Portal to create an account or reset your password.

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Viewing the Discovery Environment Dashboard

The Dashboard provides an overview of recent activity inside CyVerse and the Discovery Environment. Here you can see CyVerse-related news and events, video tutorials, and newly released public apps. Also, items specific to you will appear here, such as your recently launched analyses and newly integrated apps that you’ve been working on.

Dashboard

Some of the sections available in the Dashboard

  • CyVerse News: Newsfeed of latest CyVerse announcements and news articles
  • CyVerse Events: Upcoming workshops, webinars, and other events
  • CyVerse Videos: Recent releases from the CyVerse YouTube Channel
  • Recent Analyses: Recent analyses you have launched/completed
  • Recently Added Apps: New applications

Don’t see a section that interests you? Let us know through our interactive support feature Intercom.

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Managing Data in the Discovery Environment

The Discovery Environment is connected to the Data Store, allowing you to manage data and directories. To manage data in the Discovery Environment, begin by clicking on the Data icon Data Icon in the sidebar. You may be prompted to log in. Once logged in, you should see your own home directory, in order of folders first, then alphabetically.

Data Window

Browsing Data in the Discovery Environment

1. To see more information, press the Customize Columns button to show more columns in the display, such as size or modification date.

2. If the folder you’re viewing has many items in it, the bottom of the screen provides a way to change between pages and set the number of items displayed per page.

3. Click on the name of a subfolder to open that folder. Near the top of the screen, you will see breadcrumbs that indicate the folder you’re viewing and its parent folders.

4. From the top left, at the start of the breadcrumbs, you may select another root folder to view from within your home folder, “Shared With Me”, “Community Data”, and “Trash”.

Viewing Discovery Environment File/Folder Details

  1. Click the checkbox next to a file or folder to select it.
  2. With an item selected, there will be a button near the top right labeled Details. Alternatively, click the More Options menu (ellipsis) to the right edge in a file or folder’s row, and click the Details button there to see specific information about the selected item, to copy the path to the item, to add tags to the item, or to set a file’s info type.

3. Click “Permissions” to see your own permissions on the item, and those of other users.

The Discovery Environment allows you to access, view, and manage your files in the CyVerse Data Store. You can upload smaller files, but for large files or large numbers of files, we recommend faster methods such as Cyberduck or iCommands. See documentation for those tools in our Data Store Guide.

Deleting Files/Folders in the Discovery Environment

  1. If necessary, login to the Discovery Environment.

  2. To open the Data view, click on the data icon data icon on the left side of the Discovery Environment workspace.

  3. Select the desired file/folder by clicking the checkbox to its left. You can select multiple files/folders.

  4. Click on the More Options menu (ellipsis) in the upper right corner of the Data view and select delete from the pop-up menu. Once the deletion has completed, you will receive an automated notification under the notification icon notification.

    Tip

    Deleted files can be retrieved from your Trash folder. You can access the Trash folder by clicking on your username in the top left corner of the Data view.

Uploading/Importing Small Files in the Discovery Environment

  1. In the navigation menu, click the Data button Data Icon to access the Data window in the Discovery Environment.

  2. In the Data window you will see a directory of files and folders in your Data Store. You may select a folder to be the destination for your uploaded file(s). You may also click the Folder button to create a new folder. If you do not select a destination, files will be uploaded by default to your home Data Store folder (i.e., iplant/home/CYVERSE_USERNAME)

  3. Click the Upload button upload button to choose your options for importing files into the Discovery Environment:

    • To upload files from your local computer, choose Browse Local; a file browser will open and you may select up to XXX files to upload (XXX MB Max)
    • To upload files available at a URL, choose Import by URL; You may paste in a valid HTTP or an FTP URL. Then press Import. You may paste additional URLs or close this window by clicking Done.

Tip

When your Data Store file browser is open, you can also upload files from your computer by dragging them onto your browser window.

upload drag

4. Once you have begun the upload, you will get an automated notification that files have been queued for upload. You may also view the status of an upload or import by going back to the Upload button and choosing View Upload Queue.

upload queue

Note

The queue will only display the status of uploads from local files. Files imported by URL will generate a message in your notifications (bell icon, upper-right) when they have completed or if they fail.

Sharing Data with Other CyVerse User(s)

  1. If necessary, log in to the Discovery Environment.

  2. Open the Data view by clicking on Data_icon

  3. Select the data resources you wish to share with another user; then click the Share button.

  4. In the Sharing dialog that opens, ensure that the resources you wish to share are shown.

    Data_sharing

  5. In the Search field, search for the CyVerse user you wish to share with by searching for their CyVerse username or by email address.

  6. Next, under “Permission”, choose which permission you want to grant the person you are sharing these resources with.

  7. Once you are finished, click Done to begin sharing. The user(s) will be notified that resources have been shared with them and will see them in their Shared With Me folder.

    Hint

    Permissions (based on UNIX permissions) are described in this chart:

    Permission level Read Download/Save Metadata Rename Move Delete
    Read X X View      
    Write X X Add/Edit      
    Own X X Add/Edit X X X

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Searching in the Discovery Environment

Use Search to find the Apps, Analyses, and Data from anywhere within the Discovery Environment.

Searching Apps, Analyses, and Data

  1. Start searching by typing in the Search box located at the top of the page.

  2. Search will automatically begin once you have typed 3 or more characters.

  3. Search results will be displayed as a drop-down grouped by Apps, Analyses, or Data.

    Global_Search

Tip

If you want to just search Apps or Analyses or Data, use the filter drop-down next to Search field to select the appropriate filter.

  1. You can click on the desired result from the drop-down.

Tip

By default, only the top 10 results are shown. If you want to see all the results associated with a search term, hit enter key after the search term or select the option similar to View all analyses results for fasta from the results drop-down.

Detailed_Search_Results

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Using Applications in the Discovery Environment

When you are ready to analyze data, you can select from one of several hundred applications in the Discovery Environment. In this tutorial, we will cover the minimum information you need to launch an analysis using sample data. In this example, we will use the Muscle multiple sequence aligner app, to align some DNA sequences.

Browsing Apps in the Discovery Environment

To view a listing of existing applications, visit the DE Apps view, which can be accessed by clicking DE Apps Navigation Icon in the navigation bar on the left side of the DE.

When you first access the Apps view, you may be prompted to log in. After logging in, you will see a screen that looks something like this:

DE App Listing

Sorting and Filtering Applications

Click on the column headings to sort the app list in ascending or descending order by app name, the name of the person who integrated the app, or average rating. You can also use the controls at the bottom of the Apps view to choose how many apps to list on a single page and to navigate between pages.

Because the DE contains hundreds of apps, it can be helpful to reduce the number of apps that are displayed. The bar just above the app listing provides two ways to do that. First, the upper left corner of the Apps view contains the currently active subset of apps to be included in the listing. By default, the Apps view displays all apps that are available to you. By clicking the arrow next to the currently active subset, you can select a different subset of apps to display:

DE App Subsets

The currently selected app subset is highlighted in gray. The app subsets that are available are:

Application type Description
Apps under development Apps that you have added to the DE that have not been made public.
Favorite Apps Apps that you have marked as favorite apps in the DE.
My public apps Apps that you have added to the DE that have been made publicly available.
Shared with me Apps that other users have shared with you.
High-Performance Computing Apps that run at the Texas Advanced Computing Center using the TAPIS API.
Browse All Apps All apps available to you within the DE.

The second way to reduce the display of the apps list is to select a filter in the upper right corner of the Apps view. By clicking anywhere on the Filter control, you can select which type of apps you’d like to see in the listing:

DE App Filter

The currently selected filter is displayed in the Filter control itself. If no filter is selected, the control will be empty. The currently available app filters are:

Application filter Description
Agave Apps that run at the Texas Advanced Computing Center using the TAPIS API (formerly known as Agave). Choosing this filter is essentially equivalent to selecting the High-Performance Computing app subset.
DE Executable (non-interactive apps) that run on CyVerse computing resources.
Interactive Interactive apps (e.g., Jupyter, RStudio, R Shiny) and other apps with their own interactive interfaces.
OSG Executable (non-interactive apps) that run on Open Science Grid (OSG) resources.

Once you’ve selected an app filter, it will be displayed in the Filter control:

DE Selected App Filter

The selected filter will stay in place until you select a new filter or dismiss the current filter by clicking the X just to the right of the filter name. Note that the X is only present when the mouse cursor is hovering over the Filter control.

Viewing App Details in the Discovery Environment

Once you’ve found an app of interest, select it by clicking the checkbox in the row containing the app name. If exactly one app is selected, a Details button will appear in the upper right corner of the Apps view, just to the right of the Filter control.

DE App Details Button

Clicking the Details button produces a slide-out panel containing additional information about the app (e.g., description, number of times run, etc.).

DE App Details

This screen has several controls available. The Heart icon just to the right of the app name allows you to add the app to or remove it from your list of favorite apps. The heart will appear solid if the app is currently in your list of favorites. Clicking the Link icon will display a link to the app that you can copy and share with other DE users. The Stars icon labeled, Your rating, allow you to give the app a rating. The Tools used by this App tab contains information about the steps that the app takes to perform an analysis. You can dismiss the App Details view by clicking anywhere outside the panel.

Tip

Favorite your frequently used applications to make them easier to find.

Sharing Applications with Another CyVerse User

  1. If necessary, log in to the Discovery Environment.

  2. Open the Apps view by clicking on Apps_icon

  3. Select the app(s) you wish to share with another user; then click the Share button.

  4. In the Sharing dialog that opens, ensure that the apps you wish to share are shown.

    Apps_sharing

  5. In the Search field, search for the CyVerse user you wish to share with by searching for their CyVerse username or email address.

  6. Next, under “Permission”, choose which permission you want to grant the person you are sharing these apps with.

  7. Once you are finished, click Done to begin sharing. The user(s) will be notified that apps have been shared with them.

    Hint

    Permissions (based on UNIX permissions) are described in this chart:

    Permission level Launch Edit Share Make Public
    Read X      
    Write X X    
    Own X X X X

Example Discovery Environment Analysis: Multiple sequence alignment with MUSCLE

Example Data

Input Description Example
Unaligned DNA sequence reads One or more sequences in FASTA format DE_sample_plants.fas

Discovery Environment App(s):

App name Version Description App link Notes/other links
Muscle 3.8.31 Multiple sequence aligner Muscle 3.8.31  

  1. If necessary, login to the Discovery Environment.

  2. Click apps_icon Apps from the DE workspace; search for MUSCLE-3.8.31 or click this link: Muscle 3.8.31.

  3. Under “Analysis Info”, you can leave the defaults or make any desired notes.

    muscle_app_launch_info

  4. Under “Select Input Data” click Browse, then navigate to and select DE_sample_plants.fas; then click OK.

    (Location: Community Data > cyverse_training > platform_guides > discovery_environment > muscle_3_8_31 > 01_muscle_input)

    muscle_app_input_data

  5. Under “Sequence Type”, select DNA.

    muscle_app_seq_type

  6. Under the optional “Advanced Settings”, leave the default settings. If required, some analyses may be launched with requests for more minimum Resource Requirements, but this may cause those analyses to sit longer in the submission queue until a node matching those minimum requirements becomes available.

  7. Click Launch Analysis

    muscle_app_launch

    You will receive a notification and be redirected to the Analyses Listing page.

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Managing Analysis Status and History in the Discovery Environment

The Discovery Environment maintains a detailed history of jobs you have previously launched. Using the Analyses view, you can see the status of jobs in progress, cancel analyses, relaunch analyses, and view and save the parameters of previously launched analyses.

Browsing Analyses in the Discovery Environment

1. Open the Analyses view by clicking on analyses icon on the left side of the Discovery Environment workspace to monitor the status of your submitted analysis. The analysis launched most recently will appear at the top of the list.

  1. To sort your analyses, hover over the name of the column you wish to sort by and click on the arrow that appears beside the column name. Analyses can be sorted by name, start date, end date or status.
  2. To filter your analyses by user, click on the “View” dropdown menu and select either ‘only my analyses’ or ‘analyses shared with me’. The default view is ‘all’ analyses.
  3. To filter your analyses by app type, click on the “App Type” dropdown menu and select the type of analyses you would like to see (Agave, DE, Interactive, or OSG).
  4. To open the output folder of a particular analysis, click on the output folder icon output folder icon at the right side of that analysis.

Sharing Analyses with Another CyVerse User

  1. If necessary, log in to the Discovery Environment.

  2. Open the Analyses view by clicking on Analyses_icon

  3. Select the analyses you wish to share with another user; then click the Share button.

  4. In the Sharing dialog that opens, ensure that the analyses you wish to share are shown.

    Analyses_sharing

  5. In the Search field, search for the CyVerse user you wish to share with by searching for their CyVerse username or email address.

  6. Next, under “Permission”, choose which permission you want to grant the person you are sharing these analyses with.

  7. Once you are finished, click Done to begin sharing. The user(s) will be notified that analyses have been shared with them.

    Hint

    Permissions (based on UNIX permissions) are described in this chart:

    Permission level Read Download/Save Metadata Rename Move Delete
    Read X X View      
    Write X X Add/Edit      
    Own X X Add/Edit X X X

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Section Title

Some things to remember about the platform

  • reminder one
  • reminder two

Descriptive title - reference platform/tool name for searchability

  1. Replace the text below with your own

  2. Use the image src in this link to link to

    • A DE App: CyVerse_launch
    • An Atmosphere image: CyVerse_launch

  3. Click Cancel to continue is how you can show a button

  4. Tell the user to choose an appropriate value for a setting

    sample-data

    Tell them if they are following with our sample data exactly what value to choose

Summary

Next Steps:

  • Next step one
  • Next step two
More help and additional information

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Guide Maintainer(s)

Who to contact if this guide needs fixing. You can also email learning@CyVerse.org

Maintainer Institution Contact
Discovery Environment Team CyVerse / UA learning@CyVerse.org

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Tour
Data Store GUI/Command line Data Store Data Store Guide
Discovery Environment Web/Point-and-click Discovery Environment Discovery Environment Guide

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