3:53 a.m.
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>
> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com>
> 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