galaxy-dev August 2016

galaxy-dev@lists.galaxyproject.org

43 participants
72 discussions

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

3 6

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

2 1

Re: [galaxy-dev] Workflow Compatibility
by Katherine Beaulieu 27 Aug '16

27 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/ >> > >

2 7

Upgrade to Galaxy 16.07, import dumps problem
by D K 27 Aug '16

27 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!

2 8

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

1 0

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

2 1

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

1 0

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/ >> > >

1 0

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

3 3

Still an issue with PBS Pro
by SAPET, Frederic 24 Aug '16

24 Aug '16

Hello Despite the last update made to the file lib/galaxy/jobs/runners/drmaa.py I still need to modify this file in order to truncate the job name to 15 characters. I replace jobName=ajs.job_name by jobName=ajs.job_name[:15], (line 135). The line 396 (job_name = job_name[:self.restrict_job_name_length]) seems to be inefficient. Maybe I missed something ? Thank you. Fred

1 0

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galaxy-dev August 2016