SignalP Installation and Program Run Question

[lherold1]

Hello,

I was able to successfully install the program with terminal on Mac OS. I am now trying to perform the optional signalP installation. I was able to acquire the signalp file and move it into dbcan/tools. The problem I am having is after running the installation: mkdir -p run_dbcan/tools && run_dbcan/tools/ tar xzf Signalp-4.1.tar.gz && cd Signalp-4.1 it is saying permission denied. Any help on this would be appreciated.

Also, just another question I know that when you wish to run the program you have to input the fasta file name. I was wondering if there is a built in function of the program to be able to run multiple files at once or is this something that would need to be coded for separately.

Thank you

[linnabrown]

Did you do the chmod 755 to your SingnalP?

Edit the paragraph labeled "GENERAL SETTINGS, CUSTOMIZE ..." in the top of the file 'signalp'. The following twovmandatory variables need to be set:

SIGNALP     full path to the signalp-4.1 directory on your system
outputDir   where to store temporary files (writable to all users)

In addition, for practical reasons, it is possible to limit the number of input sequences allowed per run (MAX_ALLOWED_ENTRIES). For example:

###############################################################################
#               GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE
###############################################################################

# full path to the signalp-4.1 directory on your system (mandatory)
BEGIN {
    $ENV{SIGNALP} = '/home/abc/Desktop/run_dbcan/tools/signalp-4.1';
}

# determine where to store temporary files (must be writable to all users)
my $outputDir = "/home/abc/Desktop/run_dbcan/tools/signalp-4.1/output";

# max number of sequences per run (any number can be handled)
my $MAX_ALLOWED_ENTRIES=100000;

And then, use this command:

sudo cp signalp /usr/bin/signalp
sudo chmod 755 /usr/bin/signalp

[lherold1]

Hi,

I am a little bit confused by this. I'm assuming the signalp file is referring to the terminal one that is found after unzipping the .gz file.

When I open that file I do not see any section header for general settings, customize. Clarification on this would be great.

Thanks

[linnabrown]

Maybe they changed the source code recently. Let me check their newest 4.1 package.

[linnabrown]

I just install the signalp and it can works well with dbcan. There are do have those lines still in the signal file (top20 lines).

(base) lehuang@lehuang-gpu:~/Downloads/signalp-4.1$ head -20 signalp
#!/usr/bin/perl

# SignalP 4.1 main script
# 
# 2012, May 11

###############################################################################
#               GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE
###############################################################################

# full path to the signalp-4.1 directory on your system (mandatory)
BEGIN {
    $ENV{SIGNALP} = '/home/lehuang/Downloads/signalp-4.1';
}

# determine where to store temporary files (must be writable to all users)
my $outputDir = "/home/lehuang/Downloads/signalp-4.1/output";

# max number of sequences per run (any number can be handled)
my $MAX_ALLOWED_ENTRIES=100000;

[lherold1]

I was able to successfully install signalP.

Thank you for the help on this.