Hi, please make also sure the /bin directory inside of the signalp folder is in your PATH.
Things like combine-hmm-plp.awk should be included. Ciao, Bjoern Am 12.11.2015 um 15:14 schrieb Olivier CLAUDE: > Hi Peter, > > I totally agree with you about the CBS, i had so much problems to get the > files, there are so many restrictions with my university mails. > >> 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 > > For the "$SIGNALP" I just wrote what was written in the readme file, > If I open the "signalp" file, I can see on line 17 "SIGNALP=<path>/signal-3.0" > I assume that when I writ $SIGNALP it refers to this path? > My email editor changed "signalp" in"Signalp" and in"signal" in my previous > message :'( > >> Which folder were you in, and did the test/test.seq file exist relative to >> it? > > I was in "~/signal-3.0" and the file "/test/test.seq" exists. I kept the > structure from the archive, I did not wanted to change everything. > > >> But in any case, good news that signalp appears to be on your $PATH > > I had to write in in the .bashrc of my account otherwise I had to export it > everytime. > >> 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? > > I just checked and yes it seems that he is too helpful. > >> 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. > > I have only one account one this machine. Is Galaxy considered as another > user? > I installed it as a simple user, to avoid all the problems with the rights > with the root. > > Thanks again, > > Olivier > > > > -----Message d'origine----- > De : Peter Cock [mailto:p.j.a.c...@googlemail.com] > Envoyé : jeudi 12 novembre 2015 14:22 > À : Olivier CLAUDE <o.cla...@outlook.fr> > Cc : Björn Grüning <bjoern.gruen...@gmail.com>; galaxy-dev > <galaxy-...@lists.bx.psu.edu> > Objet : Re: [galaxy-dev] Tmhmm and signal P > > 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/
