Entering edit mode
4.5 years ago
aortizm
•
0
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!
A couple of questions:
(base)
. Are you using conda or any such virtual environment tool?bin
directory?bin
directory of a tool?Hi RamRS
Regards!
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.
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
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.
I already did this.Thanks.
More info needed please: What version of perl? How did you install the tool?
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!