The main concept in Bench is the “Workspace”. Multiple workspaces can be created within the project. A workspace is an instance of a Docker image that runs the framework defined in the image, such as JupyterLab, R Studio, etc. It is in this workspace that code can be written and run. Via API calls, data, analyses, Base tables and queries in the platform can be accessed and manipulated. Via the command line, R-packages, tools, libraries, IGV browsers, widgets, etc. can be installed. Data can also be graphically presented.
At the moment, each workspace runs on an individual node and are available in different resource sizes. In addition, each node will have a local storage capacity as well, where files and results can be stored temporarily, before they are stored permanently in a Project. The size of the storage capacity can range from 10GB – 64TB.
To use Bench, a workspace needs to be created. This workspace will define which docker image will be used, which node and storage size will be used, etc.
To create a new workspace:
- 1.Click + New Workspace
- 2.Complete the following fields:
- Required field
- Needs to be unique
- Docker image
- Required field
- Dropdown list is filled with all possible docker images - There are a couple of standard docker images we have provided as default docker images, but users are able to expand those docker images with new or updated packages/applications as well.
- Field is pre-filled with first option in the dropdown list
- Storage size
- Required field
- Fill out a number
- Represents the size of the storage available on the workspace. A storage from 10GB to 64TB can be provided.
- Resource model
- Required field
- Size of the machine on which the workspace will run and whether or not the machine should contain GPU.
- Access mode
- Required field
- Type of access to the internet for this workspace
- Open: Internet access is allowed
- Restricted: Internet access is restricted to software installations only
- Closed: Internet access is restricted in any capacity
- Optional field
- Provide additional information about the workspace
- 3.Click “Save”
The workspace can be edited afterwards on the Details tab within the workspace.
Workspace permissions allow users to use a Bench workspace without the need of exposing their own API key. Instead an API key belonging to the Bench workspace can be used through an environment variable. As a user you will from now on only be able to create a workspace with permissions equal to or lower than yours. These dedicated permissions will be given to your workspace to indicate what it can and cannot do within your project and are the minimal permissions that any team member needs to enter this workspace and to use it.
In case that at least one of your permissions is not high enough, you will see the following message "Your are not allowed to use this workspace as your user permissions are not sufficient compared to the permissions of this workspace". So, you won't have access to use this workspace. In case that you as a user have the same or more rights, you have 2 options. You can use the environment variable of the workspace containing the workspace's API key instead of your own API key and execute the actions for which the workspace is allowed. This API key will be renewed every time at the starting of the workspace and becomes unusable when the workspace has stopped. The other option, when you have more rights than the workpace, is to still use your own API key which allows you to do whatever your user is allowed to do based on his user permissions. The risk connected to this approach is that your personal API key can be leaked.
The permissions that a Bench workspace can receive are the following:
- Upload rights
- Download rights
- 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.
In case of an old workspace, you have the possibility to enable these workspace permissions. If enabled, you will see the same behaviour as described above. If not, the workspace will continu working as before.
To delete a workspace, click “Delete”.
The workspace will not be accessible anymore, nor 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, that you then use as a basis to start from next time, or export it using the API.
The workspace is not always accessible; it needs to be started before it can be used. From the moment a workspace is in the “Running” state, 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.
To start the workspace, follow next steps:
- 1.Go to the Details tab of the workspace
- 2.Click on Start 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.
The workspace will be paused, so content will not be accessible and actions can no longer be performed until started again. There are no resources provided at this moment. Any work that has been saved will stay stored in the meantime. Storage will continue to be charged until the workspace is deleted.
Once the Workspace is running, the Access tab should be loading the default applications. The default applications are defined by the start script part 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.
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).
NOTE: The Dockerfile commands are all run as ROOT, so it is absolutely possible to delete or otherwise 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 in any way, but inoperable Bench images will have to be deleted or fixed.
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, the same name as the original image; it is recommended to change the name
- Version: Required field, can by any value
- Description: The description you want to give your docker image (e.g., indicating which apps it contains)
- Code: The Docker file commands must be provided in this section.
The first 4 lines of the Docker file should NOT be edited. It is not possible to start a docker file with a different FROM directive. The most important 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. The building can take a while. When the 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.
From within the workspace it is possible to create a docker image and a tool from it at the same time.
- 1.Click the + Create 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 Image 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 Tool 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.
The tab mechanism allows showing a web application running on the same Bench instance to be displayed in a new window.
To create a new tab, click the (+) button next to the Activity tab. This opens a dialog box to indicate
- 1.Name: Can be any name, spaces are allowed.
- 2.URL: The app URL without the leading forward slash, but with the following slash.
Clicking Save will save the link for the tab and clicking the tab will open the new application. Clicking on the Access tab will open up the default application again.
The last tab of the workspace is the activity tab. On this tab all actions that are performed in the workspace are shown. For example, the creation of the workspace, starting of the workspace, pausing of the workspace,etc. The activities are shown with their date, the user that performed the action and the description of the action. One use of this page is to allow users 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 here the workspace the action is performed in is listed as well.