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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/