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@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 <mcrusoe@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+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@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 <mcrusoe@msu.edu>
From: Cristian Alejandro Rojas <alejandro.0317@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-b...
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@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@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>
-- *Cristian Alejandro Rojas Quintero* *Estudiante Ingeniería de Sistemas * *Universidad Distrital Francisco José de Caldas* Bogotá - Colombia