galaxy-dev March 2016

galaxy-dev@lists.galaxyproject.org

74 participants
98 discussions

IE11 display problem
by Floreline TOUCHARD 07 Mar '16

07 Mar '16

Hi Galaxy team, I try to use IE11 but I have a problem with the display : I get a blank Web page (I can only see the logo and "Galaxy" on the tab) . The javascript console gives me the same errors as described here ( https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-July/020078.html). Mostly " *Object* *doesn't** support **property** or **method* *'* *attachEvent**'*" and "*'**jQuery'* *is* *undefined*" on the files jquery.js and require.js I'm a little bit confuse. Others seem to have problems with some functionalities, but I have a problem at the beginning. Is there a way to fix it ? Thanks in advance. Floreline.

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UnicodeDecodeError with 16.01
by Anthony Bretaudeau 07 Mar '16

07 Mar '16

Hi, On our prod server that we udated to 16.01, I get this error when trying to access the list of saved histories... Do you see what's happening? Anthony URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)

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iRODS
by Mohamed Kassam 07 Mar '16

07 Mar '16

Dear all, I would like to use our interlan iRODs to pull data. I searched and i find that there is an object store for that. How it works ? DO I need to configure something else ? Thanks in advance, Mohamed

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Galaxy 15.10 Jobs not running
by Ryan G 04 Mar '16

04 Mar '16

Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file. I see in github, commits have recently been made to revert something, but I'm not clear what. Is there something going on with the job runner? Better yet, how can I track down what my issue is?

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switch to git
by Briand, Sheldon (NRC/CNRC) 04 Mar '16

04 Mar '16

Hi, I've done the recently announced security update for my running release which is 15.01. I figured I had better switch to git now while I was at it. However I'm having trouble matching revisions in git. I have looked at the instructions in the Develop/SourceCode page of the Wiki. I've used git log show-notes=hg2git after fetching them. It seems those notes stop at changeset 16698 while I am now showing changeset 17151 with the hg log -b $(hg branch) command and 17161 with hg tip. What should my next step be? Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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trouble with python packages after galaxy update
by Linda Bakker 04 Mar '16

04 Mar '16

Hi Guys, So i updated my galaxy instance to release_16.01 I usually started galaxy in a venv and used pip to install any packages my tool needed. (in this case, numpy and scipy) source my_galaxy_dir/.venv/bin/activate pip install scipy (dependency numpy also installed) ./run.sh But since the last update, i am having problems with this. Did something change? because it looks like it searches for an existing venv and then activates a new venv in my already active one?? Depending on what i try, when i execute my tool in galaxy, my messages range from ImportError: No module named scipy or ValueError: numpy.dtype has the wrong size, try recompiling <http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-the-…> I tried running galaxy without a venv, re-creating my venv. renaming my venv installing numpy, then scipy, not using pip at all. removing numpy and reinstalling without cache. I also played around with pip, doing nothing after creating my venv, or first upgrading my pip, but then after i start galaxy i get this message: (.venv)@server:/galaxy-dist$ ./run.sh Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple Collecting pip==8.0.2+gx2 Downloading https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 339kB/s Installing collected packages: pip Found existing installation: pip 8.0.3 Uninstalling pip-8.0.3: Successfully uninstalled pip-8.0.3 Successfully installed pip-8.0.2+gx2 And later on i get the message that i should upgrade my pip... I am confused...can someone tell me the correct way to start galalxy within or without my venv and how to correctly install my packages? Thanks! with regards, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker(a)wur.nl

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Fwd: Galaxy Conference
by Scott Szakonyi 04 Mar '16

04 Mar '16

Hi Martin, Thank you for the quick response! However, I'm unclear... is "Training Day One" different from the mix of individual session listed there, or does training day one consist of those other sessions that I sign up for? I have created a sched account, I'm just a bit confused about the relationship of things. Thanks! Scott On Fri, Mar 4, 2016 at 11:35 AM, Martin Čech <marten(a)bx.psu.edu> wrote: > Hello Scott, > > have you seen the schedule at https://gcc16.sched.org/ ? > > The trainings are all listed, described, and categorized there, it should > help you decide what to attend. > From my experience in addition to scientists there are many admins and > developers attending the conference so you should be able to find your > flock easily. > > Plus we are all nice. :) > > Best, > Martin > > On Fri, Mar 4, 2016 at 11:32 AM Scott Szakonyi <Scott.B.Szakonyi.1(a)nd.edu> > wrote: > >> Hi all, >> >> I know this is not a technical question per se, but this seems my best >> option for getting better information. >> >> I am planning on attending the Galaxy Conference this year. I >> administrate the Galaxy server for VectorBase (vectorbase.org), but I'm >> a computer scientist, not a bioinformatics specialist. I'm uncertain what >> would be the most informative things for me to attend... for instance, I >> see there is a training day 1 and 2, but there's no real description on the >> site of what those are. If someone could offer some guidance, I would be >> most appreciative. >> >> Also, would the conference days be useful for someone in my position? >> >> Thanks! >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu >> ___________________________________________________________ >> 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/ > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu -- 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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Galaxy Conference
by Scott Szakonyi 04 Mar '16

04 Mar '16

Hi all, I know this is not a technical question per se, but this seems my best option for getting better information. I am planning on attending the Galaxy Conference this year. I administrate the Galaxy server for VectorBase (vectorbase.org), but I'm a computer scientist, not a bioinformatics specialist. I'm uncertain what would be the most informative things for me to attend... for instance, I see there is a training day 1 and 2, but there's no real description on the site of what those are. If someone could offer some guidance, I would be most appreciative. Also, would the conference days be useful for someone in my position? Thanks! -- 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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Python 2.7 six egg fetching issue
by Yves Gagnon 04 Mar '16

04 Mar '16

Hi everyone, When I try to run galaxy using python 2.7 I get this error message while fetching eggs. Under python 2.6 I do not have that issue: DistributionNotFound: six==1.9.0 The galaxy release I use is still 15.07. Is there any fix for that other than building the egg myself, or maybe newer release do not have that issue? Thanks in advance! Yves Gagnon

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Problems with planemo functional tests
by Léo Biscassi 04 Mar '16

04 Mar '16

Hi Folks, I tried follow this tutorial [1], but I have problems in execute the command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for perform functional tests, any suggestion? Bellow some images about this problem: [image: imagem1.jpg] *Figure 1: *Command [image: imagem2.jpg] *Figure 2:* Error [image: imagem3.jpg] *Figure 3: *Galaxy Path Planemo's version is 0.23.0. [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html P.S: The command is utilized for same tool presented in tutorial. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi

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galaxy-dev March 2016