Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> Hi Björn!
>
> I do have signalP 3 , it's installed and on the path.

Good. It is a shame that CBS use a proprietary license which forbids
redistribution and packaging - otherwise I could have tried to automate
this.

> The tests files are the ones from the archive (no changes nor I tried to open 
> it manually)
>
> The exact lines in the prompt are:
>
> $SIGNALP
> Signalp -G  -t euk test/test.seq
> Gawk: fatal: cannot open file 'test/test.seq' for reading (no such file or 
> directory)
> Signal: ERROR in sequence file(s), check syntax

That's not right - the case is all inconsistent. The binary name signalp
is all lower case, so if gawk, but I infer you had something like this:

$ signalp -G -t euk does_not_exist.faa
gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot
open file `does_not_exist.faa' for reading (No such file or directory)
signalp: ERROR in sequence file(s), check syntax

Which folder were you in, and did the test/test.seq file exist relative to it?

But in any case, good news that signalp appears to be on your $PATH

> In galaxy report :
>
> Fatal error : exit code 127 ()
> /bin/sh: 1 : signal: not found
> One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > 
> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:
>

I'm guessing there is another copy-and-paste error here, with
"signal" rather than "signalp". Perhaps your email editor is
being too helpful with auto-correction?

When you ran signalp at the command line by hand, were you
doing it as the Galaxy Linux user, or with your personal account?
They probably have different $PATH settings.

>
> That's all.
> Thank you for your help again .
>
> Olivier.

Thanks Bjoern :)

Peter
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