- galaxy-dev - lists.galaxyproject.org

Error for one user when using edit properties
by SHAUN WEBB 30 Apr '10

30 Apr '10

Hi, we are having problems with a single user account. When using the 'edit attributes' button on a dataset an error is returned (traceback below). This is happening with each dataset/history. However, if the dataset is shared then properties can be edited by a different user or while logged out. It appears to be solely linked to this users account. Thanks in advance for any help. Shaun Webb When trying to 'Edit Attributes' URL: http://bifx3.bio.ed.ac.uk:8080/root/edit?id=2558 File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.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 ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/root.py', line 364 in edit all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 174 in get_legitimate_roles return sort_by_attr( [ role for role in roles ], 'name' ) File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 142 in sort_by_attr intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) AttributeError: 'NoneType' object has no attribute 'name' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Job Control in Galaxy
by Steve Taylor 30 Apr '10

30 Apr '10

Hi, We have configured our Galaxy system to use Sun Grid Engine in shared mode. We noticed that on submission of a job that running qstat does not show the jobs status. It looks the a wrapper shell script defining the environment and the command(s) is being submitted and then as far as SGE is concerned the job is done (however, the job is still running on the application server). I don't understand when using this system how you can manage submitted jobs. Isn't the point of using a queuing system like SGE that you can manage the load on the servers using the SGE configuration tool (qconf) to control the queues? Or am I misunderstanding something? Thanks for any advice, Steve

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Re: [galaxy-dev] NGS peak calling: MACS
by Vipin TS 30 Apr '10

30 Apr '10

Hi Kanwei, I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1 each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score. thnaks, Vipin T S On 27 April 2010 19:17, Kanwei Li <kanwei(a)gmail.com> wrote: > Hi Vipin, > > What is a bed wiggle file? We support both, but not at the same time :P > > Kanwei >

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What is the suggested way of adding ones own eggs/modules?
by Alexander Rose 29 Apr '10

29 Apr '10

Hi, I have successfully added my own datatype but the code for it has dependencies for additional Python modules. For now have just added them to eggs.ini to satisfy the dependencies. This works in general though I occasionally stumble upon problems when scrambling these modules. I wonder what is the suggested way of adding your own Python modules for use your own datatypes inside of galaxy? Thanks in advance. Alexander Rose

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id to output path query
by Steve Taylor 28 Apr '10

28 Apr '10

Hi, I was wondering what the id refers to in the in the history of the galaxy web interface. So for example: http://domain/root/edit?id=96 which key does this refer to and in which table? I am trying to construct a query which will return the (user generated) name of the output, the command that ran it and the path of the .dat file. Can any one give some pointers and/or point me to a schema diagram? Thanks a lot! Steve

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'cookie_path' settings in reports
by Assaf Gordon 27 Apr '10

27 Apr '10

Hi, I think the cookie_path settings is missing from the reports application. The setting is created in 'config.py' of the main galaxy, but not in the 'config.py' of the reports. The following patch fixes it. -gordon

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NGS peak calling: MACS
by Claudia Cattoglio 27 Apr '10

27 Apr '10

Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, -- Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762

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das2 server
by Davide Cittaro 26 Apr '10

26 Apr '10

Hi all, is it possible to configure galaxy to get data from a das2 server? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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problem with getting the tables up in Profile Annotations
by CHAN Chee Seng 23 Apr '10

23 Apr '10

Hi, I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the "Tables to Use" to be displayed on the web interface. I have looked at the following files. 1. annotation_profiler_options.xml 2. annotation_profiler_valid_builds.txt I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line, hg18 which is fine since I am starting with human. Where do I specify the location of my hg18? Please let me know if you need more information. Thanks for your help. Best regards, Chee Seng, Chan Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065 ------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------

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NGS peak calling: MACS
by Claudia Cattoglio 22 Apr '10

22 Apr '10

Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762

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