Need help with uploading a perl script in Galaxy local instance
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. -- Regards, JAYANT KHOPALE
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="perl">allsnp_modified.pl $input $output</command> <data name="output" format="gff3" /> etc. HTH, Vipin --
Regards, JAYANT KHOPALE
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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.ts@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="perl">allsnp_modified.pl $input $output</command> <data name="output" format="gff3" /> etc.
HTH, Vipin
--
Regards, JAYANT KHOPALE
___________________________________________________________ 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:
-- JAYANT KHOPALE
FYI the error still persists. On Mon, May 23, 2011 at 3:36 AM, Jayant Khopale <jaykhopale@gmail.com>wrote:
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.ts@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="perl">allsnp_modified.pl $input $output</command> <data name="output" format="gff3" /> etc.
HTH, Vipin
--
Regards, JAYANT KHOPALE
___________________________________________________________ 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:
-- JAYANT KHOPALE
-- JAYANT KHOPALE
Hi Jayant, FYI the error still persists.
Please find the modified tool configuration file, attached here. Just redirected your tool output to the result file in the below line <command interpreter="perl">allsnp_modified.pl $input > $output</command> HTH, Vipin
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 > instead. 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 ________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Vipin TS [vipin.ts@gmail.com] Verzonden: maandag 23 mei 2011 14:09 Aan: Jayant Khopale CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance Hi Jayant, FYI the error still persists. Please find the modified tool configuration file, attached here. Just redirected your tool output to the result file in the below line <command interpreter="perl">allsnp_modified.pl<http://allsnp_modified.pl> $input > $output</command> HTH, Vipin
Hi Alex, Indeed looking at the script.... it should be possible to use it as Vipin
indicated. However, for xml validity I wouldn't use the 'naked' > or < signs but use > instead.
Thanks for pointing it.
I am curious though on the script. Is it part of a larger script? Don't see any ARGs being read from command line.... but maybe my lack of knowledge.. ;P
Alex
I think there is a standard-in present inside the subroutine, as follows: sub process_diff { while(defined ($diff_line = <>)) ..... } regards, Vipin
Ah right. Overlooked the shortcut EMPTY <> Just not my way of doing it.. Alex ________________________________ Van: Vipin TS [vipin.ts@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 > 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
participants (3)
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Bossers, Alex -
Jayant Khopale -
Vipin TS