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January 2011

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62 discussions

GMOD Spring Training Application Deadline January 7
by Dave Clements, GMOD Help Desk 02 Jan '11

02 Jan '11

Hello all, The application deadline for the 2011 GMOD Spring Training (http://gmod.org/wiki/2011_GMOD_Spring_Training) is the end of this coming Friday, January 7. Admission is competitive, so please apply by Friday to avoid being automatically placed on the waiting list. Details are below. Thanks, and happy new year! Dave C ------- Applications are now being accepted for the 2011 GMOD Spring Training course (http://gmod.org/wiki/2011_GMOD_Spring_Training) a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD components. The course will be held March 8-12 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. These components will be covered: * Apollo - genome annotation editor * Chado - biological database schema * Galaxy - analysis and data integration framework * GBrowse - genome viewer * GBrowse_syn - synteny viewer * GFF3 - genome annotation file format and tools * InterMine - biological data mining system * JBrowse - next generation genome browser * MAKER - genome annotation pipeline * Tripal - web front end to Chado databases The deadline for applying is the end of Friday, January 7, 2011. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2010 school had over 60 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $265 (only $53 per day!). There will be a limited number of scholarships available. This may be the only GMOD School offered in 2011. If you are interested, you are strongly encouraged to apply by January 7. Links: http://gmod.org/wiki/2011_GMOD_Spring_Training http://gmod.org/wiki/GMOD_Americas_2011 http://www.nescent.org/

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Re: [galaxy-dev] galaxy command line error (fasq_grromer.py)
by Dave Clements, GMOD Help Desk 02 Jan '11

02 Jan '11

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(a)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? > -- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback

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