Workspaces

The main concept in Bench is the Workspace. A workspace is an instance of a Docker image that runs the framework which is defined in the image (for example JupyterLab, R Studio). In this workspace, you can write and run code and graphically represent data. You can use API calls to access data, analyses, Base tables and queries in the platform. Via the command line, R-packages, tools, libraries, IGV browsers, widgets, etc. can be installed.

You can create multiple workspaces within a project and each workspace runs on an individual node and is available in different resource sizes. Each node has local storage capacity, where files and results can be temporarily stored and exported from to be permanently stored in a Project. The size of the storage capacity can range from 1GB – 16TB.

For each workspace, you can see the status by the colour red is stopped, orange is started and green is running.

Once a workspace is started, it will be restarted every 30 days for security reasons. Even when you have automatic shutdown configured to be more than 30, the workspace will be restarted after 30 days and the remaining days will be counted in the next cycle.

You can see the remaining time until the next event (Shutdown or restart) in the worksapces overview and on the workspace details.

Create Workspace

If this is the first time you are using a workspace in a Project, click Enable to create new Bench Workspaces. In order to use Bench, you first need to have a workspace. This workspace determines which docker image will be used with which node and storage size.

1. Click Projects > Your_Project > Bench > Workspaces > + Create Workspace

2. Complete the following fields and save the changes.

Field	Explanation
Name	must be a unique name
Automatic Restart Reminder	The time (in days/hours) prior to an automatic restart (every 30 days) at which an email reminder for this event is sent out to the workspace owner. For example: 1d 2h
Automatic Shutdown	The time (in days/hours) between start of the workspace and automatic shutdown. For example: 5d 12h. When this value is more than 30 days, which is the restart period, the workspace will be restarted after 30 days and the remaining time will be counted in the next cycle. So for 50 days, you will have a restart after 30 days and then 20 days remaining before the workspace shuts down.
Automatic Shutdown Reminder	The time (in days/hours) prior to the automatic shutdown at which an email reminder for this event is sent out to the workspace owner. For example: 1d 2h
Docker image	The list of docker images includes base images from ICA and images uploaded to the docker repository for that domain.
Storage size (GB)	Represents the size of the storage available on the workspace. A storage from 1GB to 16TB can be provided.
Resource model	Size of the machine on which the workspace will run and whether or not the machine should contain a Graphics Processing Unit (GPU). See Bench pricing for available sizes.
Description	A place to provide additional information about the workspace.
Internet Access	Type of access to the internet which should be provided for this workspace. Open: Internet access is allowed. Restricted: Creates a workspace with no internet access. Access to the ICA Project Data is still available in this mode. Whitelisted URLs: Specify URLs* and paths that are allowed in a restricted workspace. Separate URLS with a new line. Only domains and subdomains in the specified URL will be allowed.
Access (available after selecting Docker image)	The options here are determined by the Docker image settings. The options you select will become available on the details tab of the Workspace when it is running. Web allows to interact with the workspace via a browser. Console provides a terminal to interact with the workspace.
Permissions	Your workspace will operate with these permissions. For security reasons, users will need to have the permissions matching what you set at the following permissions to run the workspace, regardless of their role. Access limited to workspace owner. When this field is selected, only the workspace owner can access the workspace. Everything created in that workspace will belong to the workspace owner. Download/Upload allowed Project/Flow/Base access

(*) URLs must comply with the following rules:

• URLs can be between 1 and 263 characters including dot (.).

• URLs can begin with a leading dot (.).

• Domain and Sub-domains:

  • Can include alphanumeric characters (Letters A-Z and digits 0-9). Case insensitive.

  • Can contain hyphens (-) and underscores (_), but not as a first or last character.

  • Length between 1 and 63 characters.

• Dot (.) must be placed after a domain or sub-domain.

• If you use a trailing slash like in the path ftp.example.net/folder/ then you will not be able to access the path ftp.example.net/folder without the trailing slash included.

• Regex for URL : [(http(s)?):\/\/(www\.)?a-zA-Z0-9@:%._\+~#=-]\{2,256}\.[a-z]\{2,6}\b([-a-zA-Z0-9@:%_\+.~#?&\/\/=]*)

Example URLs

The following are example URLs which will be considered valid.

example.com www.example.com https://www.example.com subdomain.example.com subdomain.example.com/folder subdomain.example.com/folder/subfolder sub-domain.example.com sub_domain.example.com example.co.uk subdomain.example.co.uk sub-domain.example.co.uk\

Example data science-specific whitelist compatible with restricted Bench workspaces. There are two required URLs to allow for Python pip installs:

pypi.org files.pythonhosted.org repo.anaconda.com conda.anaconda.org github.com cran.r-project.org bioconductor.org www.npmjs.com mvnrepository.com\

The workspace can be edited afterwards when it is stopped, on the Details tab within the workspace. The changes will be applied when the workspace is restarted.

Workspace permissions

When Access limited to workspace owner is selected, only the workspace owner can access the workspace. Everything created in that workspace will belong to the workspace owner.

Administrator vs Contributor

• Bench administrators are able to create, edit and delete workspaces and start and stop workspaces. If their permissions match or exceed those of the workspace, they can also access the workspace contents.

• Contributors are able to start and stop workspaces and if their permissions match or exceed those of the workspace, they can also access the workspace contents.

	create/edit	delete	start/stop	access contents
Contributor	-	-	X	when permissions match those of the workspace
Administrator	X	X	X	when permissions match those of the workspace

Setting Workspace Permissions

The teams setting determines if someone is an administrator or contributor, while the dedicated permissions you set on the workspace level indicate what the workspace itself can and cannot do within your project. For this reason, the users need to meet or exceed the required permissions to enter this workspace and use it.

For security reasons, the Tenant administrator and Project owner can always access the workspace.

If one of your permissions is not high enough as bench contributor, you will see the following message "You are not allowed to use this workspace as your user permissions are not sufficient compared to the permissions of this workspace".

The permissions that a Bench workspace can receive are the following:

• Upload rights

• Download rights (required)

• Project (No Access - Dataprovider - Viewer - Contributor)

• Flow (No Access - Viewer - Contributor)

• Base (No Access - Viewer - Contributor)

Based on these permissions, you will be able to upload or download data to your ICA project (upload and download rights) and will be allowed to take actions in the Project, Flow and Base modules related to the granted permission.

If you encounter issues when uploading/downloading data in a workspace, the security settings for that workspace may be set to not allow uploads and downloads. This can result in RequestError: send request failed and read: connection reset by peer. This is by design in restricted workspaces and thus limits data access to your project via /data/project to prevent the extraction of large amounts of (proprietary) data.

Workspaces which were created before this functionality existed can be upgraded by enabling these workspace permissions. If the workspaces are not upgraded, they will continue working as before.

Delete workspace (Bench Administrators Only)

To delete a workspace, go to Projects > your_project > Bench > Workspaces > your_workspace and click “Delete”. Note that the delete option is only available when the workspace is stopped.

The workspace will not be accessible anymore, nor will it be shown in the list of workspaces. The content of it will be deleted so if there is any information that should be kept, you can either put it in a docker image which you can use to start from next time, or export it using the API.

Use workspace

The workspace is not always accessible. It needs to be started before it can be used. From the moment a workspace is Running, a node with a specific capacity is assigned to this workspace. From that moment on, you can start working in your workspace.

As long as the workspace is running, the resources provided for this workspace will be charged.

Start workspace

To start the workspace, follow the next steps:

1. Go to Projects > your_project > Bench > Workspaces > your_workspace > Details

2. Click on Start Workspace button

3. On the top of the details tab, the status changes to “Starting”. When you click on the >_Access tab, the message “The workspace is starting” appears.

4. Wait until the status is “Running” and the “Access” tab can be opened. This can take some time because the necessary resources have to be provisioned.

You can refresh the workspace status by selecting the round refresh symbol at the top right.

Once a workspace is running, it can be manually stopped or it will be automatically shut down after the amount of time configured in the Automatic Shutdown field. Even with automatic shutdown, it is still best practice to stop your workspace run when you no longer need it to save costs.

If you want to open a running workspace in a new tab, then select the link at Projects > your_project > Bench > Workspaces > Details tab > Access. You can also copy the link with the copy symbol in front of the link.

Stop workspace

When you exit a workspace, you can choose to stop the workspace or keep it running. Keeping the workspace running means that it will continue to use resources and incur associated costs. To stop the workspace, select stop in the displayed dialog. You can also stop a workspace by opening it and selecting stop at the top right.

Stopping the workspace will stop the notebook, but will not delete local data. Content will no longer be accessible and no actions can be performed until it is restarted. Any work that has been saved will stay stored.

Storage will continue to be charged until the workspace is deleted. Administrators have a delete option for the workspace in the exit screen.

The project/tenant administrator can enter and stop workspaces for their project/tenant even if they did not start those workspaces at Projects > your_project > Bench > Workspaces > your_workspace > Details. Be careful not to stop workspaces that are processing data. For security reasons, a log entry is added when a project/tenant administrator enters and exits a workspace.

You can see who is using a workspace in the workspace list view.

Workspace Tabs

Access tab

Once the Workspace is running, the default applications are loaded. These are defined by the start script of the docker image.

The docker images provided by Illumina will load JupyterLab by default. It also contains Tutorial notebooks that can help you get started. Opening a new terminal can be done via the Launcher, + button above the folder structure.

Docker Builds tab (Bench Administrators only)

To ensure that packages (and other objects, including data) are permanently installed on a Bench image, a new Bench image needs to be created, using the BUILD option in Bench. A new image can only be derived from an existing one. The build process uses the DOCKERFILE method, where an existing image is the starting point for the new Docker Image (The FROM directive), and any new or updated packages are additive (they are added as new layers to the existing Docker file).

The Dockerfile commands are all run as ROOT, so it is possible to delete or interfere with an image in such a way that the image is no longer running correctly. The image does not have access to any underlying parts of the platform so will not be able to harm the platform, but inoperable Bench images will have to be deleted or corrected.

In order to create a derived image, open up the image that you would like to use as the basis and select the Build tab.

• Name: By default, this is the same name as the original image and it is recommended to change the name.

• Version: Required field which can by any value.

• Description: The description for your docker image (for example, indicating which apps it contains).

• Code: The Docker file commands must be provided in this section.

The first 4 lines of the Docker file must NOT be edited. It is not possible to start a docker file with a different FROM directive. The main docker file commands are RUN and COPY. More information on them is available in the official Docker documentation.

Once all information is present, click the Build button. Note that the build process can take a while. Once building has completed, the docker image will be available on the Data page within the Project. If the build has failed, the log will be displayed here and the log file will be in the Data list.

Tools (Bench Administrators Only)

From within the workspace it is possible to create a tool from the Docker image.

1. Click the Manage > Create CWL Tool button in the top right corner of the workspace.

2. Give the tool a name.

3. Replace the description of the tool to describe what it does.

4. Add a version number for the tool.

5. Click the Docker Build tab.

   • Here the image that accompanies the tool will be created.

   • Change the name for the image.

   • Change the version.

   • Replace the description to describe what the image does.

   • Below the line where it says “#Add your commands below.” write the code necessary for running this docker image.

6. Click the General tab. This tab and all next tabs will look familiar from Flow. Enter the information required for the tool in each of the tabs. For more detailed instruction check out the Tool creation section in the Flow documentation.

7. Click the Save button in the upper, right-hand corner to start the build process.

The building can take a while. When it has completed, the tool will be available in the Tool Repository.

Workspace Data

To export data from your workspace to your local machine, it is best practice to move the data in your workspace to the /data/project/ folder so that it becomes available in your project under projects > your_project > Data. Although this storage is slow, it offers read and write access and access to the content from within ICA.

• For fast read-only access, link folders with the CLI command workspace-ctl data create-mount --mode read-only.

• For fast read/write access, link non-indexed folders which are visible, but whose contents are not accessible from ICA. Use the CLI command workspace-ctl data create-mount --mode read-write to do so. You can not have fast read-write access to indexed folders as the indexing mechanism on those would deteriorate the performance.

Every workspace you start has a read-only /data/.software/ folder which contains the icav2 command-line interface (and readme file).

File Mapping

Activity tab

The last tab of the workspace is the activity tab. On this tab all actions performed in the workspace are shown. For example, the creation of the workspace, starting or stopping of the workspace,etc. The activities are shown with their date, the user that performed the action and the description of the action. This page can be used to check how long the workspace has run.

In the general Activity page of the project, there is also a Bench activity tab. This shows all activities performed in all workspaces within the project, even when the workspace has been deleted. The Activity tab in the workspace only shows the action performed in that workspace. The information shown is the same as per workspace, except that here the workspace in which the action is performed is listed as well.