I've uploaded a compressed (gzip) fastq file into galaxy. The file is recognized as fastq. When I try to run the FASTQ Summary Statistics program on the uploaded file, I don't see the file listed in the drop-down box.
I then tried to change the type of the file from fastq to fastqillumina and I get the following error:
⇝ TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given)
URL: http://genomes.umdnj.edu/galaxy/library_common/ldda_edit_info?library_id=223... File '/opt/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given)
Hi all - I've had a series of problems with a vanilla installation of Galaxy and no response from the mailing list...I could use some help with getting Galaxy running properly...
Ryan Golhar wrote:
I've uploaded a compressed (gzip) fastq file into galaxy. The file is recognized as fastq. When I try to run the FASTQ Summary Statistics program on the uploaded file, I don't see the file listed in the drop-down box.
I then tried to change the type of the file from fastq to fastqillumina and I get the following error:
⇝ TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given)
URL: http://genomes.umdnj.edu/galaxy/library_common/ldda_edit_info?library_id=223...
File '/opt/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given)
Hi Ryan,
I've uploaded a compressed (gzip) fastq file into galaxy. The file is recognized as fastq. When I try to run the FASTQ Summary Statistics program on the uploaded file, I don't see the file listed in the drop-down box.
This is because all Galaxy tools that use fastq as an input data type require fastqsanger format. Use the FASTQ groomer to convert your fastq file into fastqsanger format, and the resulting dataset will be available for summary statistics. More information on basic fastq manipulations, including grooming, can be found in this screencast:
http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html
I then tried to change the type of the file from fastq to fastqillumina and I get the following error: ⇝ TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given)
This is bug. We'll fix it soon and notify you when it's fixed so that you can update your repository.
Thanks for using Galaxy, J.
galaxy-user@lists.galaxyproject.org
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Jeremy Goecks -
Ryan Golhar