June 2014 - galaxy-dev - lists.galaxyproject.org

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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Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location
by Hans-Rudolf Hotz 04 Jun '14

04 Jun '14

As far as I know, there is no reference to the path of the datafiles in the 'database' (no matter whether it is SQLite, MySQL, or PostgreSQL) - may be the Galaxy developers can confirm this? If you wanna be on the safe side, work with a sym link, and don't change the entry in the 'universe_wsgi.ini' file. Hans-Rudolf On 06/04/2014 09:14 AM, Neil.Burdett(a)csiro.au wrote: > Thanks Hans-Rudolf, > would this also be the same case for PostgreSQL database? i.e. we can move the database/files somewhere else , change universe_wsg.ini and all would be good? There is no link from the database to where the flat files are stored? > > cheers > Neil > ________________________________________ > From: Hans-Rudolf Hotz [hrh(a)fmi.ch] > Sent: Wednesday, June 04, 2014 5:11 PM > To: Burdett, Neil (CCI, Herston - RBWH) > Subject: Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location > > Hi Neil > > First a little comment: I strongly suggest to switch over to PostgreSQL. > > Keep in mind that the 'database' (in your case the SQLite database) does > not contain any data. The 'database' contains just the meta data and the > users data which is required to run Galaxy. > > "#file_path = database/files" is the location where the data sets are > stored. You can copy the contents of "~/database/files/ to a new > location and make the appropriate changes in 'universe_wsgi.ini' or set > up a sym link. > > > I hope this helps/clarifies > > Regards, Hans-Rudolf > > > > > > > On 06/04/2014 04:49 AM, Neil.Burdett(a)csiro.au wrote: >> 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 >> >> >> ___________________________________________________________ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >>

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Fwd: Re: Move galaxy/database (SQLite) to a new location
by Hans-Rudolf Hotz 04 Jun '14

04 Jun '14

oops - forget to keep it on the list -------- Original Message -------- Subject: Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location Date: Wed, 04 Jun 2014 09:11:00 +0200 From: Hans-Rudolf Hotz <hrh(a)fmi.ch> To: Neil.Burdett(a)csiro.au Hi Neil First a little comment: I strongly suggest to switch over to PostgreSQL. Keep in mind that the 'database' (in your case the SQLite database) does not contain any data. The 'database' contains just the meta data and the users data which is required to run Galaxy. "#file_path = database/files" is the location where the data sets are stored. You can copy the contents of "~/database/files/ to a new location and make the appropriate changes in 'universe_wsgi.ini' or set up a sym link. I hope this helps/clarifies Regards, Hans-Rudolf On 06/04/2014 04:49 AM, Neil.Burdett(a)csiro.au wrote: > 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 > > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

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Move galaxy/database (SQLite) to a new location
by Neil.Burdett＠csiro.au 03 Jun '14

03 Jun '14

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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