Hi All,
As I checked TMHMM-2.0 - redirect it is said:
NOTE: TMHMM-2.0 is outdated. A more recent and better transmembrane predictor, DeepTMHMM, has been released and is available at https://services.healthtech.dtu.dk/service.php?DeepTMHMM.
Can we consider adding DeepTMHMM into usegalaxy.eu?
Correct, the current version of this tool that is wrapped for Galaxy is:
Then, I traced back through the links to check on the status and to gather some details. I was suspecting a licensing issue, but let’s confirm.
Toolshed repository → https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
README at the development repository → pico_galaxy/tools/protein_analysis/README.rst at master · peterjc/pico_galaxy · GitHub
SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological Sequence Analysis at the Technical University of Denmark, http://www.cbs.dtu.dk/cbs/
Following the link redirects to another README.
The Health Tech Service site runs our current web services.
If you are academic, you can download the software for free and you are encouraged to do so.
Following this next link points to a list of analysis tools and the details for each.
DeepTMHMM Prediction of transmembrane helices in proteins
Finally (!!), we now find the licensing requirements.
This software is made freely available here for both academic and commercial purposes. Download instruction can be found here.
For commercial users wishing to run the software on their own servers, a commercial license is required. This is not needed for academic users. To inquire about a commercial license, please contact licensing@biolib.com.
What this means
This updated/new tool version does not appear to be fully open source. It is free, but the authors grant a license to each commercial user running the software on other resources. Some Galaxy users would be doing this, and this type of license can prevent the use of tools at public Galaxy servers … but not always!
Sometimes the authors will allow for a checkbox on the tool form instead to declare that a tool is being used for academic/non-commercial reasons. That said, this tool’s license is a bit different than the others we currently host (that I know of). Specifically, I haven’t seen a commercial use declaration choice included on a tool form (yet).
What to do
We can make a request to the IUC to see what they think. Maybe someone is already planning on creating a new tool wrapper (or adapting the current wrapper). And, maybe the licensing issues can be mitigated. Or, they may already know that this isn’t possible (for now).
Would you like to do this, or would you like me to get it started?
The process involves opening a new ticket in the Issues section of this repository. Be sure to include a link to the details to help the developers to review. You can also include a link to this topic as another reference.
Hopefully this helps! If you decide to create the ticket, please consider linking it back here so others finding our topic can follow the updates! 