Help with TMHMM

Question

[aortizm]

Hi people!

I'm trying install TMHMM in my computer (ubuntu 18.04), but I have some error when run tmhmm

this error:

(base) iim-unah@iimunah-Precision-7820-Tower:~/tools/tmhmm/bin$ ./tmhmm seq.fasta
syntax error at ./tmhmm line 13, near "$opt_basedir:"
Unknown regexp modifier "/t" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/h" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/e" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/T" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/h" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/h" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/e" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/T" at ./tmhmm line 13, at end of line
Unknown regexp modifier "/h" at ./tmhmm line 13, at end of line
./tmhmm has too many errors.

I modified all the parameters indicated in the manual (perl Path, and basedir, in my case home/tools/tmhmm) but I'm not sure if I did it right.

if anyone can help me, I'll appreciate it very much.

Thank!

[Ram]

A couple of questions:

1. Your command line prompt says (base). Are you using conda or any such virtual environment tool?
2. Why are you running the tool from within its bin directory?
3. Why is your input file in the bin directory of a tool?

[aortizm]

Hi RamRS

1. in this case I am not using any virtual tool, I have conda, but I use it for other softwares.
2. I am running it from the bin just for testing the software and not having to type long commands for the location of the files.
3. same as above. if yo can help me, I will thank you very much.

Regards!

[Ram]

I have conda, but I use it for other softwares

You're using it right now. You're in the conda base environment. You might want to disable auto-loading conda base environment.

I just read the TMHMM install README, and it looks like really badly designed software. Can you add the bin directory to your PATH and try running it outside the bin dir? I know it shouldn't make a difference, but you can never predict what happens with badly designed software.

[kishorssf91]

Hi Ram,

I also have the same issue. I also tried escaping from conda. But it produced only a blank folder. Can you give any other suggestion? Thanks

[Ram]

Sorry, it's been a long time since I looked into this specific problem and I don't use TMHMM, so I won't be able to help you. You could start a new post and link to this post on the new one for context. That way, people who know TMHMM would be able to help you out.

[kishorssf91]

I already did this.Thanks.

[Joe]

More info needed please: What version of perl? How did you install the tool?

[aortizm]

Hi Joe

I have perl 5 installed in my compute, and installed TMHMM with the instruction in the readme file

If you can help me, I will appreciate it very much.

regards!