Hi Michael,

I was just looking for the khmer Galaxy wrappers in order to try
diginorm on some high coverage data, but they are not yet in
the main ToolShed are they? I found this on the Test Tool Shed:

https://testtoolshed.g2.bx.psu.edu/view/crusoe/khmer

The last update date seems to match the changes here:
https://github.com/ged-lab/khmer/tree/master/scripts/galaxy

Thanks,

Peter

(I know you were suggesting moving the Galaxy wrappers out
of the khmer repository and under the IUC tools repository,
https://github.com/galaxyproject/tools-iuc/issues/1 - do you
still want to do that, or keep it under the group's own GitHub?)

On Thu, Jan 9, 2014 at 4:12 AM, Michael R. Crusoe <mcru...@msu.edu> wrote:
> 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.0...@gmail.com> 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 <mcru...@msu.edu>
>>>
>>> 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-...@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
>>
>>
>>
>>
>> --
>> Cristian Alejandro Rojas Quintero
>> Estudiante Ingeniería de Sistemas
>> Universidad Distrital Francisco José de Caldas
>> Bogotá - Colombia
>>
>
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