Re: [galaxy-dev] Some plugin for digital normalization
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
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
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>
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
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
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 <mcrusoe@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.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-me...
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
-- Cristian Alejandro Rojas Quintero Estudiante Ingeniería de Sistemas Universidad Distrital Francisco José de Caldas Bogotá - Colombia
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participants (3)
-
Cristian Alejandro Rojas -
Michael R. Crusoe -
Peter Cock