Partek Flow allows an administrator to configure the system through the Settings menu. This section will describe the following sections:

• System Information

• System Preferences

• LDAP Configuration

Aside from System information, these sections can only be viewed using a Partek Flow administrator account.

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

Partek Flow user accounts can be tied to an organization’s Lightweight Directory Access Protocol (LDAP) database. These can be configured by administrator accounts using the LDAP Configuration menu (Figure 1). Click on the icon to edit the LDAP configuration. Enter the settings relevant to your domain. Consult with your organization’s LDAP database administrator for assistance with configurations. For more information about any of the fields, mouse over the .

Once the LDAP settings have been successfully configured, proceed to the User management section of the Settings page then click on . The Source field should denote the name of the LDAP configuration entered. Typing a few characters of the username will prompt Partek Flow to suggest users that are available in your LDAP database to add.

Additional Assistance

The System preferences menu accessible to administrator accounts (Figure 1) allows you to configure Partek Flow preferences. These preferences generally govern the activities of other users within the Partek Flow server. They can only be viewed and configured by Administrator accounts. The preferences are subdivided into the following sections:

• [General preferences](#general preferences)

Modifying preferences under the User quotas and limitations section require the User Disk Quotas license. Upon opening the system, all sections are collapsed except for Filesystem and storage (Figure 1).

Figure 1. System Preferences Page

Filesystem and storage

Data download directory

• Specifies the directory on the server to which the data files will be uploaded

Library file directory

• Specifies the directory on the server to which the library files will be uploaded

Default project output directory

• If Sample file directory is selected, files will be written on the same directory in which the sample files are located

• If Other is selected, a directory on the server must be specified to which the project output files will be written

• The user can override this setting by specifying the output directory in the project’s Data tab after at least one sample has been created

• If Enforced private directory is selected, files will be written on the user's private directory. The alternative folder specified after else will be used if no private directory is assigned to a user.

Store file-path symbolic links

• If Yes is selected, Partek Flow will store new file paths with any symbolic links intact, making it easier to change where the links point. Otherwise, new paths are stored with symbolic links replaced by the directories to which they point, guaranteeing that Partek flow can uniquely identify each file and recognize when it already has information about that file. Changing the setting does not affect file paths already stored or the ability of Partek Flow to locate earlier files

Activity log retention

• Number of months activity logs are kept for

Task queue and job processing

Figure 2. Editing the Task queue and job processing preferences

Start Internal worker at Partek Flow server startup

• When enabled, an internal worker will be started upon server restart

Maximum running projects

• Sets the maximum number of projects that will run simultaneously. Any tasks already running will be completed before this takes into effect

Adjust job nice value

• Niceness value that is added to Partek Flow commands. Higher values are nicer. Set to 0 to disable

Show anonymous tasks on the queued tasks page

• If Yes is selected, all users can view the tasks queued up on the server and tasks that are not shared with the user will appear as anonymous

Show warning when no workers are connected

• If Yes is selected, a warning will be displayed when no workers are attached to the Partek Flow server

Email admins long running queued task

• If Yes is selected, Partek Flow will email admins (Figure 3) if a running task has a remaining runtime longer than the specified days and adding more workers could speed up the task

Figure 3. Example of an email sent to Partek Flow administrators for predicted long runtimes

User quotas and limitations

Figure 4. Editing User quotas and limitations preferences

Only administrators can manage library files

• If Yes is selected, only administrators can import and delete library files and regular users can only view library files

Only administrators can create system-wide attributes

• If Yes is selected, only administrators can create system-wide attributes within projects

Upload file size limit

• Size limit for files that can be uploaded using the My computer option

• Setting this to 0 removes file size limit

• Sets the default size of disk quota available for all users

• Disk quotas for specific users can be set in the User management page

• If Set as the quota for users having none is checked, disk quotas are retroactively set for all users currently without disk quotas

• Selecting None means there are no disk quotas across all users

• Specifies the actions when user reaches 80% of their disk quota

• An email can be sent to the user and/or the administrators (Figure 5)

• The user can also be prevented from importing additional samples and running tasks until they clear additional space

Figure 5. Example of an email sent to Partek Flow administrators about user quota

• Specifies the actions when user reaches their disk quota

• An email can be sent to the user and/or the administrators (similar to Figure 5)

• The user can also be prevented from importing additional samples and running tasks until they clear additional space

Authentication settings

Figure 6. Configuring Authentication settings

Days for user to set password

• If a user requests a password reset, this specifies amount of time the user has to reset their password

Use proxy server

• Allows administrator to configure proxy settings for the Partek Flow server

• Note that port number changes require a corresponding update to tomcat/conf/server.xml and a Partek Flow server restart

Allow users to override the default session timeout

• If checked, this gives each user the ability to override the default session timeout with their own settings as specified in "My preferences"

Default session timeout

• The amount of time, in minutes, before users are automatically logged out

• This protects users in the event that they walk away from their computer

Require HTTPS for all pages

• If checked, this requires HTTPS to load Partek Flow pages. Specify HTTPS port

Email settings

These settings allow Administrators to use the embedded email server within Partek Flow. Select the checkbox to configure mail server (Figure 7).

Figure 7. Configuring Email settings

Email users on transfer of project ownership

• Administrators can configure whether email notifications are sent when project ownership is transferred. By selecting the relevant checkbox, the new or previous project owner can be notified.

Extra text to email to new users

• If the Email users on creation checkbox is selected, new Partek Flow users will receive an email with a link to set their password within Partek Flow. The email will include this extra text, which may have URLs in it. This setting does not affect user accounts that come from LDAP, because these accounts use the password stored in LDAP, not in Partek Flow

General preferences

Figure 8. Editing General preferences

Data table decimal precision

• Specifies the number of decimal places displayed

Additional Assistance

The System information page can be found in Settings>System information (Figure 1).

For new users, Partek Flow provides sample RNA-Seq data available for download. To download the files, select the corresponding data set under Download tutorial data. Depending on the dataset you select, this will automatically create a new project either called Brain vs UHR or iDEA Challenge.

After the data has finished downloading, the samples will automatically be imported into the project. See our for more information.

Partek Flow details displays the build version currently installed in your server as well as your Root and Library directories, the architecture version and the internet browser you are currently using.

Server details lists additional information about the server that Partek Flow is installed in. Java details lists the version of Java and its configuration as used by Partek Flow. On the other hand, Partek Flow license details lists the licenses available for use in your Partek Flow server.

Figure 1. System information page when viewed by a regular user

Additional Assistance