Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance

[Jayant Khopale]

Hi,

Thanks! I have removed the white spaces. I am actually a beginner in Perl so
kindly bear with me. However I have one doubt, could it be because of the
usage of the redirection operator used in the usage of the perl script?
Kindly let me know. Regards.

On Mon, May 23, 2011 at 3:16 AM, Vipin TS vipin...@gmail.com wrote:

 Hi Jayant,

 Hi,

 I am trying to upload a Perl script into Galaxy however it gives me an
 error  *TypeError: 'NoneType' object does not support item assignment*.
 It seems that there is a mismatch between the input and output arguments and
 the file formats specified. I would really be thankful if someone can help
 me with this. Thanks in advance. Attached is the perl script, the
 configuration file for the perl script and the global tool_conf.xml file.


 Could you please consider to remove the white-space from your tool
 configuration file *methylation-snp.xml


 *for ex:
 command interpreter=perlallsnp_modified.pl $input $output/command
 data name=output format=gff3 / etc.

 HTH, Vipin

 --
 Regards,
 JAYANT KHOPALE

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JAYANT KHOPALE
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Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance

[Bossers, Alex]

Ah right. Overlooked the shortcut EMPTY 
Just not my way of doing it..
Alex


Van: Vipin TS [vipin...@gmail.com]
Verzonden: maandag 23 mei 2011 17:39
Aan: Bossers, Alex
CC: Jayant Khopale; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Need help with uploading a perl script in Galaxy 
local instance

Hi Alex,

Indeed looking at the script it should be possible to use it as Vipin 
indicated.
However, for xml validity I wouldn't use the 'naked'  or  signs but use gt; 
instead.


Thanks for pointing it.

I am curious though on the script. Is it part of a larger script? Don't see any 
ARGs being read from command line but maybe my lack of knowledge.. ;P

Alex


I think there is a standard-in present inside the subroutine, as follows:

sub process_diff {

while(defined ($diff_line = ))
.
}

regards, Vipin


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