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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