Hello Ken, Portions of the Galaxy distribution from bitbucket are required to run fastq_groomer.py on the command line. Specifically, obtain the source and then add galaxy/lib to your PYTHONPATH. usage: fastq_groomer.py input_file input_type output_file output_type output_quality_score_encoding summarize_input where input_type and output_type can each be one of: sanger illumina solexa cssanger output_quality_score_encoding can be: ascii decimal None summarize_input can be: summarize_input dont_summarize_input Hopefully this will get you going, but please let us know if we can help more, Thanks, Jen Galaxy Team On 8/16/10 7:22 AM, kenlee nakasugi wrote:

Hi All,

I'm new to NGS analysis, and command line analysis for that matter. (I'm in the process of learning perl/python - so please bear with this newbie query). I've installed the fastx-toolkit and the scripts here are working great, but couldn't find the fastq_groomer script anywhere on the galaxy page, at http://hannonlab.cshl.edu/fastx_toolkit/index.html, nor on the web, except from this page: http://bitbucket.org/galaxy/galaxy-dist/src/tip/tools/fastq/

I tried running it via: python fastq_groomer.py input_file input_type output_type as per the fastq_groomer.xml, but doesn't work.

Is this the correct fastq_groomer script, am I running it correctly, or where can I get this script to run like the other fastx-toolkit scripts? I know I could use the Galaxy server/ or install galaxy locally, but for several reasons at the moment want to use the individual scripts.

Thanks in advance!

Ken

Kenlee Nakasugi School of Molecular Bioscience University of Sydney

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