Sharing data in IRIDA

Once you’ve got data into IRIDA, either by web upload or from a sequencing facility with the uploader tool, you’re probably going to want to share that data with collaborators.

In order to share data from a project, you must have the Manager role on the project. The Manager role implies ownership of the data contained in the project. You can find out if you have the Manager role by looking at the project members section.

You can share data with collaborators in IRIDA in two ways: to an individual user account, or to a group of user accounts.

If the individual person you want to share with within IRIDA does not have a user account, you must also have permission to create a user account for that user. If you do not, then you’ll need to contact someone who has permissions to create user accounts.

Creating a User Account

If the person you would like to share data with within IRIDA does not have a user account, you’ll need to make an account for them.

You may create a new user account in IRIDA if you have the Manager or Administrator system role.

After logging in to IRIDA, click on the Users menu, and select “Create User”:

Create user menu.

Fill in the user details fields. All fields are required for a user account in IRIDA:

User details form.

By default, a user will be issued a randomly-generated, one-time-use key to activate their account. The first time the user logs in, they will be required to change their password. You may manually enter a user password by unchecking “Require User Activation”:

Manual password entry.

Passwords must meet the following requirements:

If you manually set a password for a new user account, the user will not be required to change their password on first log in.

When you click “Create User”, an e-mail will be sent to the user (to the e-mail address you entered) including the URL for IRIDA (as configured in the Administrator Install Guide). If you did not manually set a password for the user, the e-mail will include a link to activate the user account:

User welcome e-mail.

On successfully creating a new user account, you will see the user details that you entered:

User details page.

Creating a User Group

You may share data with groups of users in IRIDA by creating a user group.

All users are permitted to create user groups in IRIDA.

After logging in, click on the Settings menu and select “Create Group”:

Create user group menu.

Fill in the group details fields. Only the group name is required, but you can optionally provide a more detailed description of what the user group is:

User group details form.

On successfully creating a new user group, you will see the user group details that you entered:

User group details page.

By default, your user account is assigned to the group as the group owner.

You can add other users to the group by clicking on the “Add Group Member” button:

Add group member button.

In the dialog that appears, choose the user that you want to add and the group role that the user should have. Group owners are allowed to add new members to the group. Group members are not allowed to add new members to the group.

Add group member dialog.

Adding a Project Member

Once the user account or group is created, go to the project containing the data you want to share with this user, and select the Members tab.

Project details members tab.

Adding an Individual Member

To add an individual project member, click on the “Add Member” button:

Add project member button.

You can use the dialog that appears to select a user account, and choose the Project Role that the new member should have:

Add project member dialog.

Remember: a project collaborator has read-only permissions, and a project manager is allowed to modify project details.

Once you’ve selected the user and role to add to the project, click on the “OK” button.

Adding a Group Member

To add a group to the project, click on the “Groups” button on the left-side of the page, then click on “Add Group”:

Add project group member button.

You can use the dialog that appears to select a user group, and choose the Project Role that the new group member should have:

Add project group member dialog.

Remember: a project collaborator has read-only permissions, and a project manager is allowed to modify project details. When adding a user group, all members of the user group will have that project role on this project.

Note: If a user is added both as an individual member and as part of a group, the individual user project role takes precedence over the group project role. For example, if Bob is added to Project 5 as a Project Owner as an individual member, and is in a Group that’s on Project 5 as a Project Member, Bob would be given Project Owner permissions to Project 5.

Once you’ve selected the user group and role to add to the project, click on the “OK” button.

Downloading Sample Data

All project members are allowed to export the samples in a project to the command line (add a link to the command line tutorial), to Galaxy (add a link to the Galaxy tutorial) or to download sample data. External collaborators will most likely want to download sample data to their own computer so that they can manage the data locally. External collaborators can use IRIDA to download multiple samples in a zip package or they can download individual files by examining each sample.

Downloading Multiple Samples

You may download all of the files in a sample, or even download the files from multiple samples, by selecting the samples that you want to download, clicking on the “Export” button just above the samples list and clicking on “Download”:

Samples download button.

IRIDA will provide you with a zip file containing the sequencing data for all of the selected samples. You can extract the files from the zip archive using the command-line program unzip, using the built-in Windows extractor tool, or using a program like 7-zip

WARNING: sequencing data can make for a very large download, especially when downloading all of the sequencing data for a project. We strongly recommend that you do not download data to your PC, especially if you are going to be using Linux command-line tools and the command-line export tool option is available.

Downloading Individual Files

To view details about an individual sample, start by viewing the samples in a project, then click on the sample name in the samples table:

Sample name button.

The sample details page shows all of the details that are currently known about a sample:

Sample details page.

Start by viewing the details of an individual sample. On the sample details page, click on the “Files” tab, just above the sample details panel:

Sample details file tab.

Sequence files may have been uploaded as paired-end files or as single-end files, depending on how the isolate was sequenced.

Single-end files will appear in the sample alone:

Single-end sequencing file.

Paired-end files will appear in a pair:

Paired-end sequencing file.

Quality control information for a sequence file may appear below the file:

File QC

You can download a sequence file by clicking on the icon, on the right-hand side of the row for the sequence file.