- galaxy-dev - lists.galaxyproject.org

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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Can't display tools in the middle panel of Galaxy
by Stephanie LE GRAS 13 Sep '16

13 Sep '16

Hi there (again again), The last problem we are facing is that sometime when clicking on a tool name in the tool panel, the form don’t get displayed in the middle panel. We’ve checked the log of galaxy and it seems that the HTML request arrives but nothing happens. We have noticed that this seems to occur more ofter when the history is empty and we can correct the phenomenon if we use a non empty url such as : http://use.galaxeast.fr/root?job_id=c72a8935c65f68c1 or if we load an history and click on the [i] (view details) of a dataset. Versions of Galaxy : release_16.04 (production instance), release_16.07 (test instance). 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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Galaxy Proteomics Hackathon
by Björn Grüning 10 Sep '16

10 Sep '16

Hi all! I would like to spread the news from the GalaxyP team about a new hackthon. Please join and help us if you have some time! ********************* The first Galaxy-P CONDA hackathon will be held on September 27th and 28th. Galaxy-P and proteomics tool developers will participate in this hackathon to "CONDA-package" some of the prioritized proteomics tools within Galaxy. The hackathon will be an online event which will start with an introduction to Galaxy structure and CONDA packaging by Bjoern Gruening. https://github.com/galaxyproteomics/tools-galaxyp/issues/57 Details soon. Please see if you would like to publicize this. Thanks and Regards, Pratik

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delete user and all trace of user
by Fernandez Edgar 09 Sep '16

09 Sep '16

Hello gents! I’ve successfully got my version 16.04 up and running and everything is still there (user, groups roles, data and tools). Unfortunately , I’m still having a problem with deleting a user. I’ve purge him and then I deleted him. but, he still shows up in my list of users as "purged". Is there a way to completely remove him from galaxy? Do I need to run a script in a cron job to clean my galaxy periodically? Thanks in advance! Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568

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How to set up handler and web server process within a virtual machine
by Katherine Beaulieu 08 Sep '16

08 Sep '16

Hi Everyone, I am looking to set up a web server and handler process for galaxy within a virtual machine. I've tried following the instructions written here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#Starting_an… But, I can still start Galaxy with sh run.sh, also the commands associated with supervisord don't seem to work, I keep getting this error: "Error: positional arguments are not supported:" Lastly, how can I confirm that this is working? Will I see two 'python' processes running when I run top? Katherine

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Html page in galaxy-dist
by Mohamed Kassam 08 Sep '16

08 Sep '16

Dear all, I've created different pages in html and php, and I put them in apache by changing the port. Now I changed the SSL certifcate and I moved galaxy web adress to https. However my other page are not recognized because they are still in http. Do you know where I can put my php and html pages in galay-dist can be picked up by apache like the welcome.html files then I can transfer them to https. Thanks in advance, Mohamed

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Converting an internal user to an external user
by Ryan G 07 Sep '16

07 Sep '16

Hi all - I'm having a problem with a user account and Galaxy getting confused with it being internal vs external. When we first set up galaxy, we were using Galaxy's internal authentication system. This worked well but all our users then had another password to keep track of. We activated external user authentication a few months ago and it works fine for us. This user hasn't logged in since and recently tried but is unable to. I discovered her account in Galaxy appears as an internal account eg created before we were using external authentication. Now that we have external authentication, Galaxy doesn't recognize her and she gets the user_disabled page whenever she tries to log in. Is there a way I can change her account in Galaxy from being an internal to an external account? Ryan

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