- galaxy-dev - lists.galaxyproject.org

Galaxy migration to docker environment
by Matthias De Smet 29 Aug '16

29 Aug '16

Hi all, We’re looking to migrate our Galaxy instance from a VM based solution to a docker based solution. Therefore, we need to move all our user and reference data. What is the best possible solution to migrate all data and change the path of said data in the database? Thanks! M

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Putting it all together - toolshed tool + conda dependency
by Steve Cassidy 29 Aug '16

29 Aug '16

Hi all, I’m making baby steps towards having a repeatable installation for my tools. But I’m now stuck, so help would be appreciated. I have a tool that works and is in the test toolshed (alveoimport in Data Sources). It depends on my python package which is now part of bioconda (pyalveo, version 0.6). I can run my tool via planemo, which works I think because I have pyalveo installed in a local venv. If I try to run the docker image (derived from bgruening/galaxy-stable but with the testtoolshed added) I am able to install my tool, but it doesn’t pick up the dependency, so it doesn’t work. I tried running with planemo turning on conda dependency resolution (following https://pypi.python.org/pypi/planemo/) planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution . It seems to have a go, but fails: galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency shell command for dependency 'pyalveo' galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo version 0.6 galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve dependency on 'pyalveo', ignoring So, what’s the easiest route to a Galaxy deployment with my tool installed. The Docker route would be best I think, but what do I have to add to bgruening/galaxy-stable to have conda find my dependencies. Thanks in advance, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Loading a GUI on galaxy
by Lijo John 29 Aug '16

29 Aug '16

Hello All, I want to know, whether it is possible to embed graphical user interface like that of WEKA VisualizePanel tool in galaxy ? I am able to load the GUI on a local instance of galaxy. But when i am trying to access the galaxy server through a remote connection, this GUI is not able to load on remote desktop. Any comments or suggestions would be of great interest ! -- Regards, Lijo John

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Re: [galaxy-dev] Workflow Compatibility
by Katherine Beaulieu 26 Aug '16

26 Aug '16

On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > I think I did not explain myself well. I meant that if I have a tool that > takes multiple file paths and outputs multiple Galaxy datasets to the > history, would this tool be workflow compatible, meaning capable of being a > part of any workflow? From the behaviour I am getting now I am assuming it > isn't but I just wanted to confirm that this isn't supported functionality. > > On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> Hi Katherine, >> >> Are you asking about compatibility staying on the same Galaxy >> instance, or the harder problem of compatibility sharing workflows >> between Galaxy servers? >> >> Taking data from input Galaxy datasets should be fine, anything else >> may not be portable. Even the relatively simple case of using >> datafiles referenced via an example.loc file (e.g. BLAST databases) >> would require the entries in the example.loc file be synchronised >> between Galaxy instances, and the associated data files too. >> >> Peter >> >> >> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Hi Everyone, >> > Would anyone be able to tell me the conditions which would make a tool >> > non-workflow compatible? I have a tool that imports files from a third >> party >> > application and auto-detects the file format. There is also the option >> to >> > upload multiple files at once so the tool always uploads at least two >> files. >> > From what I have described can anyone see why this tool would not be >> able to >> > send one of its files to the next tool in the chain, ex. a text >> manipulation >> > tool? >> > Thanks, >> > 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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Upgrade to Galaxy 16.07, import dumps problem
by D K 26 Aug '16

26 Aug '16

Hi Galaxy-devs, I just tried upgrading to 16.07 from 16.01 and get this error when starting up: > Traceback (most recent call last): > File "./scripts/paster.py", line 26, in <module> > serve.run() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 1061, in run > invoke(command, command_name, options, args[1:]) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 1067, in invoke > exit_code = runner.run(args) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 223, in run > result = self.command() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 639, in command > app = loadapp( app_spec, name=app_name, relative_to=base, > global_conf=vars) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 292, in loadapp > return loadobj(APP, uri, name=name, **kw) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 317, in loadobj > return context.create() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 755, in create > return self.object_type.invoke(self) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 274, in invoke > filtered = context.next_context.create() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 755, in create > return self.object_type.invoke(self) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 191, in invoke > return fix_call(context.object, context.global_conf, > **context.local_conf) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 94, in fix_call > val = callable(*args, **kw) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", > line 39, in app_factory > return paste_app_factory( global_conf, **kwargs ) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", > line 76, in paste_app_factory > webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/web/framework/webapp.py", line > 115, in add_ui_controllers > module = import_module( module_name ) > File "/opt/rh/python27/root/usr/lib64/python2.7/importlib/__init__.py", > line 37, in import_module > __import__(name) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", > line 16, in <module> > from galaxy.util.json import dumps > ImportError: cannot import name dumps Any suggestions? Thanks!

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The new Galaxy release July 2016 Galaxy Release (v 16.07) is out!
by Jennifer Hillman-Jackson 26 Aug '16

26 Aug '16

July 2016 Galaxy Release (v 16.07) <https://wiki.galaxyproject.org/News/2016_07_GalaxyRelease> The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the *July 2016 (v16.07) release of Galaxy <https://docs.galaxyproject.org/en/master/releases/16.07_announce.html>*. *Reminders* - Python 2.6 is no longer supported. Details: 16.01 release announcement <https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease> - The Galaxy source is no longer hosted on Bitbucket. Details: 16.04 release announcement <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/releases/16.04_…> . *Highlights <https://docs.galaxyproject.org/en/master/releases/16.07_announce.html#highl…>* [image: Inline image 1] *Get Galaxy <http://getgalaxy.org/>* [image: Inline image 2] On behalf of the Galaxy Core and Contributor team <https://wiki.galaxyproject.org/GalaxyTeam> (and community), *Thanks for using Galaxy!* -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org

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Workflow Compatibility
by Katherine Beaulieu 26 Aug '16

26 Aug '16

Hi Everyone, Would anyone be able to tell me the conditions which would make a tool non-workflow compatible? I have a tool that imports files from a third party application and auto-detects the file format. There is also the option to upload multiple files at once so the tool always uploads at least two files. From what I have described can anyone see why this tool would not be able to send one of its files to the next tool in the chain, ex. a text manipulation tool? Thanks, Katherine

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Loading GUI on galaxy
by Lijo John 26 Aug '16

26 Aug '16

Hello, I want to know, whether it is possible to embed graphical user interface like that of WEKA VisualizePanel tool in galaxy ? I am able to do it on a local instance of galaxy. But when i am trying to access the server (in which galaxy is installed) this GUI is not able to load on remote desktop. John

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Re: [galaxy-dev] Parameter Storing in Database
by Katherine Beaulieu 25 Aug '16

25 Aug '16

On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > No actually I meant in what file is the table job_parameter getting filled > during execution? > Katherine > > On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: > >> You mean the stuff for the tool-data tables? As I understand it, it is >> loaded in: >> >> lib/galaxy/tools/data/__init__.py >> >> There's a ToolDataTableManager and a TabularToolDataTable (with >> associated TabularToolDataField). >> >> Peter >> >> On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu < >> katherine.beaulieu014(a)gmail.com> wrote: >> >>> Would anyone be able to tell me in what file the storing of tool >>> parameters into the database occurs? >>> Thanks! >>> 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/ >> >> >> ___________________________________________________________ >> 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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problem with local toolshed
by Vincent Cahais 25 Aug '16

25 Aug '16

Hello, I cannot use my toolshed anymore because of a bug. The service is running, but the web page display this error : Module galaxy.web.framework.middleware.error:151 in __call__ >> <http://galaxy.iarc.fr:9009/#> app_iter = self.application(environ, sr_checker) Module paste.recursive:85 in __call__ >> <http://galaxy.iarc.fr:9009/#> return self.application(environ, start_response) Module galaxy.webapps.tool_shed.framework.middleware.hg:218 in __call__ >> <http://galaxy.iarc.fr:9009/#> return self.app( environ, start_response ) Module paste.httpexceptions:640 in __call__ >> <http://galaxy.iarc.fr:9009/#> return self.application(environ, start_response) Module galaxy.web.framework.base:131 in __call__ >> <http://galaxy.iarc.fr:9009/#> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> <http://galaxy.iarc.fr:9009/#> body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:1963 in index >> <http://galaxy.iarc.fr:9009/#> status=status ) Module galaxy.web.framework.webapp:858 in fill_template >> <http://galaxy.iarc.fr:9009/#> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework.webapp:872 in fill_template_mako >> <http://galaxy.iarc.fr:9009/#> return template.render( **data ) Module mako.template:445 in render >> <http://galaxy.iarc.fr:9009/#> return runtime._render(self, self.callable_, args, data) Module mako.runtime:829 in _render >> <http://galaxy.iarc.fr:9009/#> **_kwargs_for_callable(callable_, data)) Module mako.runtime:864 in _render_context >> <http://galaxy.iarc.fr:9009/#> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:890 in _exec_template >> <http://galaxy.iarc.fr:9009/#> callable_(context, *args, **kwargs) Module _base_base_panels_mako:123 in render_body >> <http://galaxy.iarc.fr:9009/#> __M_writer(unicode(self.left_panel())) Module _webapps_tool_shed_index_mako:166 in render_left_panel >> <http://galaxy.iarc.fr:9009/#> __M_writer(filters.html_escape(unicode(trans.app.shed_counter.generation_time ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 2: ordinal not in range(128) Thanks, Vincent

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