GeneTrail is a comprehensive web-based application to perform Gene Ontology and pathway analysis, with a user-friendly graphical interface. It is not possible, however, to access it programmatically, which can be cumbersome when processing more than a few datasets. It is nevertheless possible to automate interactions with the graphical interface using iMacros, which works as an add-on to web browsers such as Firefox.
iMacros is very simple to use:
- Once installed, open iMacros in Firefox.
- Click on “Record” and perform all the tasks you normally do on GeneTrail, including upload and download. Stop recording when done.
- The macro is now saved and you should see it in the iMacros panel. Right click on it and edit as follows:
- Locate the name of the file to be uploaded and replace it by a new file name.
- Add “WAIT SECONDS=120″ before the line starting with “ONDOWNLOAD”. If necessary, replace 120 with a number of seconds greater than the time GeneTrail takes to process results, so iMacros waits long enough before to try downloading.
- Edit the line starting with “ONDOWNLOAD” to indicate the folder and file names (e.g. “ONDOWNLOAD FOLDER=/home/sebastien/imacrosresults FILE=result1.zip WAIT=YES”). Delete other lines starting with “ONDOWNLOAD”, if any.
- Click on play. To replay with different upload and download file names, edit the script as indicated above.