SignalP is adding the extraneous "bin"

Question

[jamie.pike]

I have been going through the process of installing SignalIP. I am trying to run the following command on the test data:

 ./bin/signalp -fasta test/euk10.fsa -org euk -format short -prefix euk_10_short

from this directory

1983390@vettel:~/apps/signalp-5.0b$   pwd
/home/u1983390/apps/signalp-5.0b

It produces this output:

SignalP-5.0. Starting fasta file reading...
Total proteins read: 10.
Organism: euk.
Starting protein prediction...
2020/06/22 16:23:08 asset: open /home/u1983390/apps/signalp-5.0b/bin/bin/signalp: no such file or directory

It seems like like SignalP is adding the extraneous "bin". The path signalp-5.0b/bin/bin/signalp is used when it should be signalp-5.0b/bin/signalp.

I don't understand why it is appearing twice. If I run the command signalp -fasta test/euk10.fsa -org euk -format short -prefix euk_10_short the output is signalp: command not found.

How do I fix this?

Answer 1

[Mensur Dlakic]

I don't have the access to SignalP v5.0 and maybe they changed something from v4.1 that I have. In 4.1 signalp is a perl script that needs to be customized. Specifically, early on in that script one must enter a correct installation directory, which in your case appears to be /home/u1983390/apps/signalp-5.0b. After doing that and specifying temporary directory, within that installation directory you run it by adding ./ in front of signalp:

./signalp -fasta test/euk10.fsa -org euk -format short -prefix euk_10_short

Alternatively, you can copy signalp to a directory that is in your path, or add /home/u1983390/apps/signalp-5.0b to your $PATH variable. Then you will be able to run it without ./ from anywhere on your system.

[jamie.pike]

Thank you for your advice. Adding /home/u1983390/apps/signalp-5.0b/bin to my .bash_profile seems to have worked.