Hi Olivier, On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.claude@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