> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com&gt; > Date: December 26, 2013 2:37 AM > To: galaxy-dev(a)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/normaliz... 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+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 mcrusoe(a)msu.edu @ the Genomics, Evolution, and Development lab; Michigan State University http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe

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+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.0317(a)gmail.com&gt; 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 <mcrusoe(a)msu.edu&gt; > > > From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com&gt; >> > Date: December 26, 2013 2:37 AM >> > To: galaxy-dev(a)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/normaliz... >> >> 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+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 >> mcrusoe(a)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 mcrusoe(a)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>

That is wonderful to hear. I'm adding more khmer Galaxy wrappers and the next release of khmer will have the necessary modifications included. Please let me know if there is a specific feature you'd like to see. On Jan 8, 2014 11:09 PM, "Cristian Alejandro Rojas" <alejandro.0317(a)gmail.com&gt; wrote: > > Sorry for the late answer. > > Thank you so much Michael. > > I have tested the plugin and everything now works fine! > > Cheers > > > 2013/12/29 Michael R. Crusoe <mcrusoe(a)msu.edu&gt; >> >> 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... >> >> And I've updated the code base. You'll need to run the following to >> update your installation >> >> >> pip install -e >> git+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.0317(a)gmail.com&gt; 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 <mcrusoe(a)msu.edu&gt; >>> >>>> > From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com&gt; >>>> > Date: December 26, 2013 2:37 AM >>>> > To: galaxy-dev(a)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/normaliz... >>>> >>>> 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+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 >>>> mcrusoe(a)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 >> mcrusoe(a)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 > ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/