WoLFPSort Installation

Question

[Patadu94]

Hi all,

I am trying to run EffHunter on my university cluster command line and and reading the README.txt file I am told to install other software. I managed to install SignalP, Phobious, TMHMM but I am having trouble with WOLFPSort.

I am looking at the GitHub repository but I cannot figure out what does it mean the first steps. I have made a quick search online, and did not find any link to download the tar.gz file. Do any of you used EffHunter and encountered the same problem? How can I solve it?

Thanks

Answer 1

[dthorbur]

I don't see any reference to a tar.gz in the installation guide for WolfPSort. They have compiled binaries, which you can use either by cloning the whole repo, or just downloading specific files. The executables in binary-i386 are compatible with Ubuntu 22.04.

That said, EffHunter is just a wrapper for several existing tools. It is relatively easy to make your own version of it with more current tools. It would require writing a script to manipulate each output into a single file, but that's it. I would suggest replacing WolfPSort with something like DeepLoc2, and maybe add a clustering algorithm like MMseqs.

[Patadu94]

Indeed, I just find out on Google that there is no tar.gz file. However, I have downloaded a .zip file that should contain everything about WOLFPSort from GitHub and loaded into EffectorP, following the READ.ME.txt file. Because of some errors, I could not make it run yet.

Not being an informatician makes it very difficult to modify the code as you suggested. That's why I was looking into way to make EffHunter run as it is described on GitHub.

[dthorbur]

Ah, there isn't much more I can do to help then unfortunately. The codebase for EffHunter is more than 4 years old, so you might struggle to get it running anyway as minor changes to any of the tools can result in errors.

As mentioned, EffHunter is simply a wrapper. So you could generate each of the relevant files using the web servers where available (SignalP, TargetP, DeepLoc, TMHMM, all are available on the same website), then it's simply merging dataframes which is a very simple task in R or Python, or can be done in excel, but will be far more tedious. Might be worth learning some basic scripting, it goes a long way.