Hi Peter, Thanks for all. $ arch
x86_64
$ uname -a >Linux LM1166 3.16.0-38-generic #52~14.04.1-Ubuntu SMP Fri May 8 09:43:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $ which perl >/usr/bin/perl $ perl -v > This is perl 5, version 18, subversion 2 (v5.18.2) built for x86_64-linux-gnu-thread-multi (with 41 registered patches, see perl -V for more detail) (...) $ /usr/bin/perl -v > This is perl 5, version 18, subversion 2 (v5.18.2) built for x86_64-linux-gnu-thread-multi (with 41 registered patches, see perl -V for more detail) (...) NOTE: You have to pipe the input file into this tool, it does not take the input argument as a filename: $ runWolfPsortSummary animal test.fasta Command Line Parsing Error; Do not know what to do with argument "test.fasta" Usage: runWolfPsortSummary [*OPTIONS*] *organismType* runWolfPsortSummary (--usage|--help|--man) Pipe sequences in from standard in. In your case it seems to be failing to even give this error message, apparently due to not finding one of the Perl files it comes with, line 37 is: use fastafmt::GetOptWarnHandler; Question: Where did you put the tool? Is there a .../bin/fastafmt/ folder? Is there are .../bin/fastafmt/GetOptWarnHandler.pm file? I did not changed the structure of the tools as you recommanded it in the python script. olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ ls binByPlatform psortModifiedForWolfFiles runWolfPsortSummary.py checkFastaInput.pl README test.fasta fastafmt runAddAlignmentToHtml testQuery.fasta GetOptWarnHandler.pm runWolfPsortHtmlTables wolfPredict pod runWolfPsortSummary WoLFPSORTpredictAndAlign olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin/fastafmt $ ls GetOptWarnHandler.pm What happens if you try to do this: $ cd /path/you/put/wolfpsort $ ./runWolfPsortSummary animal <~/repositories/pico_galaxy/test-data/four_human_proteins.fasta It gives me : olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta sh: 1: /bin/checkFastaInput.pl: not found sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found /home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error opening file: "/bin/../data//animal.wolfw" Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile utilityMatrixFile I tried with different options : olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary --print-neighbors animal <~/galaxy/test-data/four_human_proteins.fasta sh: 1: /bin/checkFastaInput.pl: not found sh: 1: /bin/psortModifiedForWolfFiles/psortModifiedForWoLF: not found /home/paulh/cbrcRepos/C++/utils/argvParsing/ArgvParser.hh:291 Error opening file: "/bin/../data//animal.wolfw" Usage: /bin/wolfPredict [OPTIONS] weightFile trainingDataFile utilityMatrixFile Or olivier@LM1166 ~/galaxy/CBS/WoLFPSort-master/bin $ runWolfPsortSummary --print-all-score animal <~/galaxy/test-data/four_human_proteins.fasta Error in parsing command line. Perhaps problem with "--print-all-score" Usage: runWolfPsortSummary [*OPTIONS*] *organismType* runWolfPsortSummary (--usage|--help|--man) Pipe sequences in from standard in Regards, Olivier -----Message d'origine----- De : Peter Cock [mailto:p.j.a.cock@googlemail.com] Envoyé : vendredi 4 décembre 2015 11:16 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : galaxy-dev@lists.galaxyproject.org Objet : Re: [galaxy-dev] wolfpsort Hi Olivier, First of all, let's double check what kind of machine you are running, in case that gives us some clues: $ arch $ uname -a Let's double check which Perl you have, $ which perl $ perl -v $ /usr/bin/perl -v NOTE: You have to pipe the input file into this tool, it does not take the input argument as a filename: $ runWolfPsortSummary animal test.fasta Command Line Parsing Error; Do not know what to do with argument "test.fasta" Usage: runWolfPsortSummary [*OPTIONS*] *organismType* runWolfPsortSummary (--usage|--help|--man) Pipe sequences in from standard in. In your case it seems to be failing to even give this error message, apparently due to not finding one of the Perl files it comes with, line 37 is: use fastafmt::GetOptWarnHandler; Question: Where did you put the tool? Is there a .../bin/fastafmt/ folder? Is there are .../bin/fastafmt/GetOptWarnHandler.pm file? What happens if you try to do this: $ cd /path/you/put/wolfpsort $ ./runWolfPsortSummary OrganismType should be one of {"fungi", "plant", "animal"} pipe fasta query sequences in from standard in Usage: runWolfPsortSummary [*OPTIONS*] *organismType* runWolfPsortSummary (--usage|--help|--man) Pipe sequences in from standard in. Or, with a real test - for example using one of the test files I often use: $ cd /path/you/put/wolfpsort $ ./runWolfPsortSummary animal < ~/repositories/pico_galaxy/test-data/four_human_proteins.fasta # k used for kNN is: 32 sp|Q9BS26|ERP44_HUMAN extr 18, E.R. 5, plas 3, mito 2, lyso 2 sp|Q9NSY1|BMP2K_HUMAN nucl 25, cyto_nucl 17, cyto 7 sp|P06213|INSR_HUMAN extr_plas 11.5, plas 10.5, extr 9.5, pero 5, E.R. 4 sp|P08100|OPSD_HUMAN plas 32 Regards, Peter On Fri, Dec 4, 2015 at 9:13 AM, Olivier CLAUDE <o.claude@outlook.fr> wrote:
Hello again,
I cannot launch it manually neither. It gives me the same error… :
runWolfPsortSummary animal test.fasta
Can't locate fastafmt/GetOptWarnHandler.pm in @INC (you may need to install the fastafmt::GetOptWarnHandler module) (@INC contains: /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl . /bin) at /bin/runWolfPsortSummary line 37.
BEGIN failed--compilation aborted at /bin/runWolfPsortSummary line 37.
I think i missed something somewhere. Any lead?
thanks