You are doing nothing wrong Cristian, it was my error. I've updated the tool definition file; it is now at https://github.com/ged-lab/khmer/blob/output_naming1 /scripts/normalize-by-median.xml
And I've updated the code base. You'll need to run the following to update your installation pip install -e git+...@github.com:ged-lab/khmer.git@output_naming1#egg=khmer or if you don't have a github account: pip install -e git+ https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer To be able to use diginorm inside Galaxy Workflows we are only supporting diginorming into a single file at this time. There is a chaining method where multiple files can be processed sequentially but until Galaxy supports proper collections a cleaner integration will have to wait. Interested parties can follow along at https://github.com/ged-lab/khmer/pull/237#issuecomment-31307144 On Thu, Dec 26, 2013 at 10:53 PM, Cristian Alejandro Rojas < alejandro.0...@gmail.com> wrote: > Thank u michael. > > I downloaded and install khmer to my machine, the i have include your > galaxy plugin in my local instance, but when I try to run this from the web > interface i'm getting this error: > > Traceback (most recent call last): > File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line > 123, in prepare_job > job_wrapper.prepare() > File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in > prepare > self.command_line = self.tool.build_command_line( param_dict ) > File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in > build_command_line > command_line = fill_template( self.command, context=param_dict ) > File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in > fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File > "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-i686-ucs4.egg/Cheetah/Template.py", > line 1004, in __str__ > return getattr(self, mainMethName)() > File "cheetah_DynamicallyCompiledCheetahTemplate_1388113247_46_38074.py", > line 111, in respond > NotFound: cannot find 'hashsize' > > I have tried change parameters, using the default parameters, advanced > parameters but it didn't work. Do you know what am i doing wrong? > > Cheers! > > > 2013/12/26 Michael R. Crusoe <mcru...@msu.edu> > > > From: Cristian Alejandro Rojas <alejandro.0...@gmail.com> >> > Date: December 26, 2013 2:37 AM >> > To: galaxy-dev@lists.bx.psu.edu >> > Subject: [galaxy-dev] Some plugin for digital normalization >> >> > Hello all, >> > >> > I've been searching in tool sheds(main and test) for a plugin to do >> digital normalization of reads, for example Trinity has one script to do >> this (./util/normalize_by_kmer_coverage.pl), diginorm is another >> alternative (http://ged.msu.edu/papers/2012-diginorm/). >> > >> > Do you know if there is a galaxy tool ready for this work or should I >> develop my own? >> >> Hello Cristian, >> >> I am actively working on a wrapper for normalize-by-median.py and the >> other tools in the khmer suite. >> >> >> https://github.com/ged-lab/khmer/blob/galaxy-integration/scripts/normalize-by-median.xml >> >> It requires some changes on our end which you can track here: >> >> https://github.com/ged-lab/khmer/pull/237 >> >> You can install this branch of khmer via pip >> >> pip install -e git+...@github.com:ged-lab/khmer.git@output_naming1 >> #egg=khmer >> >> or if you don't have a github account: >> >> pip install -e git+ >> https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer >> >> (Instructions on installing using a virtualenv or on OS X are at: >> https://khmer.readthedocs.org/en/latest/install.html just substitute in >> the pertinent pip line from above) >> >> I haven't tested it much; doing so is the top of my to-do list for the >> rest of this week. If you or anyone else is feeling adventurous I would be >> happy to have the feedback. >> >> Cheers! >> >> -- >> Michael R. Crusoe: Software Engineer and Bioinformatician >> mcru...@msu.edu >> @ the Genomics, Evolution, and Development lab; Michigan State University >> http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 >> @biocrusoe >> > > > > -- > *Cristian Alejandro Rojas Quintero* > *Estudiante Ingeniería de Sistemas * > *Universidad Distrital Francisco José de Caldas* > Bogotá - Colombia > > -- Michael R. Crusoe: Software Engineer and Bioinformatician mcru...@msu.edu @ the Genomics, Evolution, and Development lab; Michigan State University http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe<http://twitter.com/biocrusoe>
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