[Gmod-help] Re: [galaxy-dev] galaxy command line error (fasq_grromer.py)

[Florent Angly]

Hi Gilgi,

If you read the beginning of the fastq_groomer.py file, you can see that 
this script takes 5 mandatory arguments (input_filename, input_type, 
output_filename, output_type, force_quality_encoding) and an optional 
argument (summarize_input):

>     input_filename = sys.argv[1]
>     input_type = sys.argv[2]
>     output_filename = sys.argv[3]
>     output_type = sys.argv[4]
>     force_quality_encoding = sys.argv[5]
>     summarize_input = sys.argv[6] == 'summarize_input'
>     if force_quality_encoding == 'None':
>         force_quality_encoding = None

Your problem is likely that you provided only 4 arguments.

In my eyes, the FASTQ tools lack two things that can be an issue when 
running the script through the command line:
1/ There is no help manual that describes what the tools does and what 
arguments it takes
2/ The scripts do not check that the mandatory arguments were provided 
by the user

Best,
Florent


On 02/01/11 16:34, Dave Clements, GMOD Help Desk wrote:
> I am forwarding your question to the Galaxy Dev list, which is the
> best place to ask this type of question.
>
> Dave C
>
> On Tue, Dec 28, 2010 at 11:27 PM,<gilgi.friedlander at weizmann.ac.il>  wrote:
>> Hi,
>>
>> I am trying to run locally the fastq_groomer.py
>>
>> My command:
>>
>> python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt illumina seq_out.txt sanger
>>
>> seq.txt is a fastq file with Illumina qualities.
>>
>> I get the following error:
>>
>> Traceback (most recent call last):
>> File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 37, in<module>
>> if __name__ == "__main__": main()
>> File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 10, in main
>> force_quality_encoding = sys.argv[5]
>> IndexError: list index out of range
>>
>> Does anyone know what the problem is?
>>
>
>