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.c...@googlemail.com]
Envoyé : vendredi 4 décembre 2015 11:16
À : Olivier CLAUDE <o.cla...@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.cla...@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
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