Open a fisheye lens image in Photoshop
Open the Actions Palette click on add new Action Set Icon in the botton of the Actions Palette looks like a folder name it ImageProcessor Actions
Click on add New Action Icon in bottom of the Actions Palette name it lens correction click record.
Use Photoshop menu Filter>Lens Correction... In the Lens Correction dialog make all the setting required for your Fisheye lens and click OK
Click on the Stop recording button in the Actions Palette
Hightlight the Action set you just recorded the action into in the Actions Palette
Use the Actions Palette fly-out menu in the upper right corner of the Actions Palette item Save Actions and save your action.
Scripts and actions run inside Photoshop not outside.... Also Lens Correction in Photoshop is done by a Photoshop Filter Plug-in that runs from within Photoshop. I quite sure you used this indirectly when you used menu File>Automate>Lens Correction... which runs a an Automate script "Lens Correct.jsx" the lens correction plug-in is also used indirectly within a PhotoMerge stack from the stack script "LensCorrect.exv".
If your images are within a single file system tree you can point the Image Processor script at the root and check include all subfolders also point the Image Processor at your action and where you want the new files saved then click Run. Then go on vacation perhaps when you return from vacation all the images files will have been processed. Using Links within the file system tree you may even be able to process more then a single tree. If your images are from more then one Fisheye lens types and focal length. You may have to script the Lens Correction Plugin like done in the Automate Lens Correction script. "Lens Correct.jsx" there is a large comment in it that may help you understand how to do that.