- galaxy-dev - lists.galaxyproject.org

2014 Galaxy Community Conference June 6 Registration Deadline (this Friday)
by Dave Clements 04 Jun '14

04 Jun '14

Hello all, Regular registration for the 2014 Galaxy Community Conference (GCC2014, https://wiki.galaxyproject.org/Events/GCC2014) closes this Friday, June 6. After that late registration is still open, but registration rates *go up 100%.* GCC2014 is all about high-throughput biology. It's in Baltimore, from June 30 through July 2. The full program is posted, and includes - Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> - 15 sessions on 12 topics in 5 parallel tracks with topics ranging from *Visualizing NGS data *to* Galaxy installation and administration* - 26 talks <https://wiki.galaxyproject.org/Events/GCC2014/Program#Day_1:_Main_Meeting.2…> including a keynote by Steven Salzberg, and 25 other talks by researchers and industry leaders - 25 Posters <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Poster_Abstracts> - and counting - we still have space for a few more <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Abstract_Submission> - Lightning Talks - Present your rsesarch in two fast paced sessions. - Birds-of-a-Feather <https://wiki.galaxyproject.org/Events/GCC2014/BoFs> - Gather with other researchers with common interests and challenges (and propose one <https://wiki.galaxyproject.org/Events/GCC2014/BoFs#Want_to_plan_a_BoF.3F> for your own area of interest) - The first ever GCC Hackathon <https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> (only 8 spaces left) Please do let us know if you have any questions. We would love to see you in Baltimore. Thanks, Dave Clements > *2014 Galaxy Community Conference (GCC2014) > <http://galaxyproject.org/GCC2014>* http://galaxyproject.org/GCC2014 > June 30 - July 2, 2014 > Homewood Campus > <http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> > > Johns Hopkins University > <http://jhu.edu/> Baltimore, Maryland > <http://visitors.baltimorecity.gov/>, United States -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy customized tool config file
by Vipin TS 04 Jun '14

04 Jun '14

Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org

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Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location
by Kandalaft, Iyad 04 Jun '14

04 Jun '14

Neil, >From what I understand, galaxy uses sqlalchemy for all its databse operations regardless of the database engine that is actually hosting the data. I suspect that galaxy uses a default sqlalchemy connection string by default even when you don't specify one, which points to databases/universe.sqlite. I also suspect that you can modify the location of the database by doing the following in universe_wsgi.ini database_connection = sqlite:////absolute/path/to/foo.db Let us know if that works. Regards, Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada From: <Neil.Burdett(a)csiro.au> To: <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] Move galaxy/database (SQLite) to a new location Message-ID: <25BF49C282C04548A60517FFB251C20D2F737E67(a)exmbx03-cdc.nexus.csiro.au> Content-Type: text/plain; charset="iso-8859-1" Hi, we have the default setup for galaxy hence using SQLite database and all data store in the same location as the galaxy install. In Universe_wsgi.ini file there is an entry # Dataset files are stored in this directory. #file_path = database/files How do we go about moving the database to a new location? We don't really want to delete the data already present in the database just move it to a new location. If we modify file_path and restart wouldn't that cause further problems as some data would be in one location and other in another location. Is it even possible to move the database once it has been created and has data in it? Thanks Neil

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Dataset_Collections : an example of code for a tool ?
by julie dubois 04 Jun '14

04 Jun '14

Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation : https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhuf… I've not yet found how to code a tool to use this collection and/or unique dataset. Is it possible to have the bowtie2 version (and or Merge Bam) with these 2 possibilities to have an example? And how can I see the icons in the formular which allow to switch between the use of unique dataset and the use of dataset collection, like is presented in the presentation ? Thanks. Julie

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Bioblend dependency error
by Nikos Sidiropoulos 04 Jun '14

04 Jun '14

Hi all, after the latest galaxy update I've experienced the following error while trying to start the server. galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in t he egg distribution. galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency "bioblend" requires "mock" Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util /pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 441, in add_ui_controllers module = import_module( module_name ) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 20, in <module> eggs.require('bioblend') File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 409, in require return c[req.project_name].require() File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 237, in require dists = self.resolve() File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (bioblend 0.4.2 (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg), Requirement.parse('mock')) First I got and error about the python module 'requests' missing, fixed it using 'pip install', and then got the error above. Regards, Nikos

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Dataset_Collections : an example of code for a tool ?
by julie dubois 04 Jun '14

04 Jun '14

Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhuf… I've not yet found how to code a tool to

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devteam packages
by Jan Kanis 04 Jun '14

04 Jun '14

Hi all, Where are the toolshed packages owned by devteam maintained? The galaxy sources don't seem to include those tool shed packages and I was unable to find a related repository on github or a similar place. Jan

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Galaxy reports crashing with the latest stable release
by bjoern.gruening＠googlemail.com 04 Jun '14

04 Jun '14

Hi, I encountered the following bug during my testing of the latest stable release: Error - <type 'exceptions.AttributeError'>: 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_da… File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 177 in specified_date_handler return self.specified_date_list_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 296 in __call__ message = message, File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1184 in fill_template def fill_template(self, filename, **kwargs): File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1199 in fill_template_mako template_lookup = template_lookup or self.webapp.mako_template_lookup File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 193 in render_get_grid_config 'info_text' : grid.info_text, AttributeError: 'SpecifiedDateListGrid' object has no attribute 'info_text' Trello card is here: https://trello.com/c/EqQCAcIe Thanks, Bjoern

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gatk2 wrapper issue
by Geert Vandeweyer 04 Jun '14

04 Jun '14

Hi, I installed the GATK2 wrapper from iuc on the lastest galaxy version. It fails to create the GATK2_PATH and GATK2_SITE_OPTIONS structures under the /tool_dependency_dir/environment_settings/ location, without a clear error (says 'never installed'). If I create the files manually, I can see them through : Admin - Manage installed toolshed repos - gatk2 - missing tool dependencies - GATK2_PATH If I click the hyperlink for GATK2_PATH here (this is the install missing dependency page), I can expand and show the GATK2_PATH / env.sh file Still, running GATK2 tools (eg UG, gives me in the logs: galaxy.jobs.handler INFO 2014-06-04 12:18:07,333 (78998) Job dispatched galaxy.tools.deps WARNING 2014-06-04 12:18:07,928 Failed to resolve dependency on 'gatk2', ignoring galaxy.tools.deps WARNING 2014-06-04 12:18:07,971 Failed to resolve dependency on 'GATK2_PATH', ignoring galaxy.tools.deps WARNING 2014-06-04 12:18:07,974 Failed to resolve dependency on 'GATK2_SITE_OPTIONS', ignoring and tool error: Unable to access jarfile /GenomeAnalysisTK.jar For my mutect_wrapper in test.toolshed, which I initially copied from the gatk2 wrapper, the exact same setup seems to work. Any help would be appreciated. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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devteam GATK v1.4 toolshed wrapper depends on java 7
by Geert Vandeweyer 04 Jun '14

04 Jun '14

Hi, Could you add java 1.7 to the dependency list of the gatk 1.4 suite in the main toolshed. Moving from built-in to toolshed version (including the downloaded jars) after the last upgrade, GATK 1.4 tools crashed on : Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(Unknown Source) at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.SecureClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.access$000(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit. adding sun-jre-7 to the PATH as first java option solved this. I thought that only gatk > 2.6 depended on java-7, so I'm not sure why this is happening. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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