September 2016 - galaxy-dev - lists.galaxyproject.org

Authentication issue
by Mohamed Kassam 16 Sep '16

16 Sep '16

Dear all I have an issue today, with authentication in our galaxy instance. I restarted our instance and now new user can not be auto register automatically. I am using the ldap of our institute, old user can login but when a new user wants to login it says user or email invalid however I saw on the terminal that ldap authentication is successful. Do you know if someone had the some issue or problem with the the database. Thanks in advance Mohamed

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Problem downloading HTML datasets
by Stephanie LE GRAS 15 Sep '16

15 Sep '16

Hi there, I’m currently facing several problems with the galaxy instance I’m managing. I’m going to send a mail per problem so sorry in advance : for flooding ! The first problem I’m facing is that we can’t download HTML datasets from Galaxy. Here is the error I got when I try to do download an HTML dataset : URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond app_iter = self.application(environ, detect_start_response) File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__ return self.handle_request( environ, start_response ) File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 245 in display return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd) File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 in display_data return self._archive_composite_dataset( trans, data, **kwd ) File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 in _archive_composite_dataset params = util.Params( kwd ) File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in __init__ self.__dict__[ key ] = sanitize_param( value ) File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in sanitize_param raise Exception('Unknown parameter type (%s)' % ( type( value ) )) Exception: Unknown parameter type (<type 'NoneType'>) We don’t want to disable the sanitize process and we try to add some tools that generate HTML datasets into the whitelist but it didn’t solve our problem. Version of Galaxy : release_16.04 Any idea about what the problem can be ? Many thanks in advance for any help, Best regards, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician GenomEast platform (former Microarray and Sequencing platform) IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

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Can't log in to Galaxy instance using Safari web browser
by Stephanie LE GRAS 15 Sep '16

15 Sep '16

Hi there (again), Another problem we are currently facing is that we cannot log in anymore on our galaxy instance using Safari. It’s working with Firefox and Chrome but when we are using Safari (with the right password and login) we just see a green box saying that we successfully logged in and we go back to the log in page. This is a problem we are encountering on our test instance that we’ve just updated to the latest release release_16.07. Any idea about what the problem can be ? Many thanks in advance for any help, Best regards, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician GenomEast platform (former Microarray and Sequencing platform) IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

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job_conf.xml and nativespecification
by Laure QUINTRIC 14 Sep '16

14 Sep '16

Hi galaxy users, while using galaxy with drmaa and real user on drm system, I would like to know if there's a way to set the variable PBS_O_LOGNAME to the real user name in the job_conf.xml : <param id="nativeSpecification">-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q test -l mem=100gb </param> Thank you, Laure

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multiqc
by Jochen Bick 14 Sep '16

14 Sep '16

Hi, I'm having trouble installing multiqc, this is the current error message: Traceback (most recent call last): File "setup.py", line 32, in <module> """.format(version)) ValueError: zero length field name in format interestingly I could install it on our developer instance which runs on 16.01 and not on your production instance 15.10. Any suggestions? Thanks Jochen

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Odd error, solution not understood
by Scott Szakonyi 14 Sep '16

14 Sep '16

Hi all, I'm getting the following error when attempting to do a trackster visualization: Error: The requested genome file (/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting! Couldn't open /vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len I found a discussion related to this error online at https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered solution actually means in terms of what I need to do. It says " You'll need to set your dataset's database/dbkey to your custom reference genome before you can visualize it". Can someone point me in the right direction to solve this issue? Thanks in advance, Scott -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Trimmomatic tool is not visible in the workflow editor
by Amarathunga A. Dineli Karunath 13 Sep '16

13 Sep '16

Hi, I have a local galaxy instance and have installed many tools from the galaxy tool shed. Recently I have installed Trimmomatic tool and installation was successful but when I go to build a workflow, trimmomatic tool is not visible in the tool panel. It works fine in all other places. Could you please help me on this? Please refer the attachments I have provided. Thanks & Regards, Dineli ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
by Katherine Beaulieu 13 Sep '16

13 Sep '16

On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Bjorn, > Thank you for taking the time to reply to my question. I don't think this > quite fits what I am trying to accomplish. I am trying to pass a set of > metadata key value pairs, where the user can have as many key value pairs > as they want, generated with a repeat parameter. I would need to pass the > entire contents of the repeat parameter to the code file to generate a > dynamic select list. Do you think this is possible? Perhaps I misread the > file you have sent me a link to. > Thanks, > Katherine > > On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning <bjoern.gruening(a)gmail.com> > wrote: > >> Hi Katherine, >> >> have a look at this one using repeats: >> >> https://github.com/bgruening/galaxytools/blob/master/tools/d >> eseq2/deseq_helper.py >> >> Ciao, >> Bjoern >> >> >> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu: >> > Hello Galaxy Community, >> > I was wondering if anyone had ever come across a situation where they >> > have had to pass the contents of a repeat parameter to a code file in a >> > Galaxy tool config? Is there any way to do this? >> > Katherine >> > >> > >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > >> > >

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apache on ubuntu
by Jochen Bick 13 Sep '16

13 Sep '16

Hi, I'm having trouble setting up the apache to redirect my local running galaxy which runs on localhost:8080 I would like that people could have access inside the lab knowing my local ip address. I read plenty of tutorials, can anyone help setting it up on Ubuntu? The files I have to modify are located at: /etc/apache2/sites-available/ 000-default.conf and default-ssl.config ? apache is up and running. Cheers Jochen

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bowtie2 data_manager issue
by Joseph Sarro 13 Sep '16

13 Sep '16

I am indexing reference genomes for bowtie2/tophat2, using the corresponding data manager. I am getting some successful indexes and others are giving an error. For the successful ones I see the genomes are appearing in the "built in index" drop down for both bowtie2 and tophat2. For the unsuccessful ones I am seeing them in the bowtie2 drop down but not tophat2. Any ideas on what could be causing this issue? The error message is as follows Thanks in advance. Traceback (most recent call last): File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1375, in finish self.tool.exec_after_process( self.queue.app, inp_data, out_data, param_dict, job=job ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2107, in exec_after_process data_manager.process_result( out_data ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/tools/data_manager/manager.py", line 303, in process_result self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 1891, in extra_files_path return self.dataset.extra_files_path File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 1707, in get_extra_files_path return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 487, in get_filename return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs) File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 508, in _call_method % ( method, str( obj ), str( kwargs ) ) ) ObjectNotFound: objectstore, _call_method failed: get_filename on <galaxy.model.Dataset object at 0x7f2584803590>, kwargs: {'dir_only': True, 'extra_dir': 'dataset_19568_files'} Tool execution generated the following error message: Unable to finish job

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