Navigate to: Admin → Integrations → Cubex
How the Integration Works
Shepherd's Cubex integration connects your practice workflows with your Cubex inventory devices. Two things sync automatically between Shepherd and your Cubex cabinet:
Patient Integration When a patient is checked into Shepherd, their record activates at the Cubex cabinet. When the SOAP is locked at the end of the appointment, the patient is deactivated and removed from the cabinet.
Profile Integration When a medication is added to the Plan (P) or Rx tab of the SOAP, the order is sent to Cubex and made available for dispensing at the cabinet.
Request more information about Cubex here
What You Need to Know
Treatments must be confirmed — not just scheduled — before orders transfer.
Selecting a treatment in the Plan is not enough — you must click Confirm Treatments for the order to transfer to Cubex.
The patient must be active at the Cubex cabinet.
Medication orders won't appear at the cabinet unless the patient is checked into Shepherd first.
Every product must be linked to a Cubex inventory item.
Each Shepherd product — including every size and dose variation — must be linked to its Cubex inventory item before orders will transfer.
Product IDs and user IDs are not visible in the UI — they're only available via CSV export.
Download the Inventory Items Report and User Report from Shepherd to get these IDs (see Setting Up the Integration below).
"Deactivate in Cubex" is a manual action — it cannot be restricted by staff role.
This button removes a patient from the cabinet before the SOAP is locked and is available to all staff — it cannot be limited by role.
Setting Up the Integration
Setup steps vary depending on your clinic's situation.
Step 1 — Send Reports to Cubex
New to Cubex: Email the Cubex pre-implementation team at preimpteam@cubex.com.
New to Shepherd, existing Cubex user: Email the Cubex integrations team at interfaces@cubex.com.
What to include in your email
Cubex will ask for specific IDs and reports from Shepherd. Here's what they need and where to find each item.
Your Clinic ID (PIMS ID) Cubex refers to this as your PIMS ID. In Shepherd, navigate to Admin → General Settings to find your Clinic ID.
Inventory Items Report This CSV contains the product IDs that Cubex uses to match medication orders to cabinet items. These IDs are not visible anywhere in the Shepherd UI — the CSV download is the only way to retrieve them.
Navigate to Reporting → Inventory Items Report → set Run Report By to Active Items → set Date & Time → select Download.
Important: Include all variations of each product — for example, every dose or size of the same medication. If a variation is missing, Cubex won't be able to match orders for that version, and they won't transfer.
User Report This CSV contains the user IDs that Cubex needs to map your staff. Navigate to Admin → Users → Users tab → click the Export Users icon.
Step 2 — Configure the Integration in Shepherd
Go to Admin → Integrations → Cubex.
Enter the credentials provided by Cubex Support:
Database Name
Database Username
Database Password
Super Admin Username
Super Admin Password
Toggle the credentials switch to Active and click Save.
Once active, you'll see an Enabled tag confirming the integration is on.
Missing credentials? Check your inbox for an email from support@cubex.com or interfaces@cubex.com. If you can't find it, contact Cubex Support.
Adding a Medication to an Existing Integration
If your clinic is already using both Shepherd and Cubex and you need to add a new medication to your cabinet configuration:
Download a fresh Inventory Items Report CSV from Shepherd — navigate to Reporting → Inventory Items Report → set Run Report By to Active Items → Download.
Email the updated report to the Cubex integrations team at interfaces@cubex.com.
Once Cubex confirms the medication has been added to your cabinet configuration, link the product in Shepherd (see Linking Products to Inventory Items below).
Note: Include all size and dose variations of the new medication in the report. Each variation needs its own entry for orders to route correctly.
Linking Products to Inventory Items
Before a Shepherd product can route medication orders to Cubex, it must be linked to the matching Cubex inventory item. Do this for every product — including all size and dose variations.
Go to Admin → Products.
Search for the product under Products and Services.
Scroll down to Link with Inventory Item and toggle it on.
Search for and select the correct inventory item.
Confirm the details and click Save.
Once linked, medication orders in SOAPs will automatically route to Cubex.
Using the Integration
Checking a patient in
Open the patient's appointment in Shepherd.
Select Check In (or set Appointment Status to Checked In).
The patient will now appear at the Cubex cabinet and is ready for medication dispensing.
Sending a medication order
Open the active patient's SOAP.
In the Plan (P) section, select the treatments to issue.
Click Confirm Treatments — the order is sent to Cubex.
Reminder: The order does not transfer until you click Confirm Treatments. A scheduled but unconfirmed treatment will not appear at the cabinet.
Sending a prescription
Go to the Rx tab of the SOAP.
Add the prescription item.
Click Save — the order is sent to Cubex.
Sending a medication request without an appointment
Add the medication in Shepherd outside of an appointment.
The patient is temporarily activated in Cubex and the order is queued for dispensing.
Checking a patient out
At the end of the appointment:
Finalize the invoice and payment.
Set the SOAP status to Locked.
The patient will be automatically deactivated and removed from the Cubex cabinet.
Deactivate in Cubex
The Deactivate in Cubex button manually removes a patient from the cabinet before their SOAP is locked. A confirmation prompt appears before the action is completed.
Use this if a patient needs to be removed from the cabinet early — for example, if a visit ends without the SOAP being locked right away.
This action cannot be restricted by staff role. It is part of the integration and does not have an independent permission setting.
At the Cubex Cabinet
Once a medication order has been sent from Shepherd:
Select the active patient at the Cubex cabinet.
Locate the order sent from Shepherd.
Click Issue, complete the Cubex dispense workflow, and retrieve the item.
Once dispensed, the order is recorded in Cubex, keeping both systems in sync.
Troubleshooting: Medication Not Appearing in Cubex
If a medication order isn't showing at the cabinet, work through these checks in order.
Is the patient active at the cabinet? The patient must be checked into Shepherd before medication orders appear. If not, check the patient in and allow a moment for the sync.
Was the treatment confirmed? In the Plan (P) section of the SOAP, confirm that you clicked Confirm Treatments. A treatment that was added but not confirmed will not transfer to Cubex.
Is the product linked to a Cubex inventory item? Go to Admin → Products, find the product, and verify that Link with Inventory Item is toggled on and the correct item is selected.
Is the correct product variation linked? Cubex matches orders using item codes tied to each specific product variation. If the exact product used in the SOAP isn't linked — for example, a different dose or size — that order won't transfer. Check that the specific product is linked, not just a similar one.
Do the item codes match on the Cubex side? If the patient is active, the treatment is confirmed, and the product is linked — but the order still isn't appearing — there may be a mismatch between Shepherd's product ID and the item code in Cubex. Contact Cubex Support with the following:
Patient name
Medication name
Shepherd product ID (from the Inventory Items Report CSV)
Date and time of the order
Need Help?
For integration setup and adding medications to your cabinet configuration: Contact the Cubex integrations team at interfaces@cubex.com.
For general support and troubleshooting: Contact Cubex Support at support@cubex.com.
Frequently Asked Questions
What is a PIMS ID and where do I find it?
PIMS ID is Cubex's name for your clinic's unique identifier in Shepherd. In Shepherd, navigate to Admin → General Settings and look for your Clinic ID — that's the value Cubex is asking for.
Can I restrict which staff can use the "Deactivate in Cubex" button?
No. The Deactivate in Cubex button is part of the integration and does not have an independent permission setting. It cannot be limited to specific staff roles.