January 2011 - galaxy-dev - lists.galaxyproject.org

how to set the width of drop down menu
by Enhai Xie 31 Jan '11

31 Jan '11

Hi All, Is there anyone who knows how to adjust the sizes of drop downs in Galaxy?. In other words, we want to set the width of drop down menu and how to do it? Thanks. __Enhai

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Workflow steps collapsible to just title bar
by Peter Cock 31 Jan '11

31 Jan '11

Dan: > Workflow steps on the run workflow page are now collapsible to > just the title bar with the tool name and annotation. Steps without > any inputs to be set will be collapsed by default. https://bitbucket.org/galaxy/galaxy-central/changeset/ec065c36cf53 Lovely - I can't remember if I asked about this or not, but it is something I was meaning to suggest. Looks good on Firefox and Safari, not tried IE yet. The only thing I'd add would be some visual clue that the title bar can be clicked on, like a little right pointing triangle as in the Mac OS X finder for folders, or a plus/minus icon like you get on tree widgets in Windows and Linux etc. Peter

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attribute holding history dataset number
by Leandro Hermida 31 Jan '11

31 Jan '11

Hello, In your history where you have a piece of data for e.g.: 1: my_file.txt The number 1 what is the attribute for that so that I can use that in a tool configuration? I tried for example $input1.dbkey but that just yields a ? mark best, Leandro

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quick question regarding text areas/boxes...
by Kostas Karasavvas 27 Jan '11

27 Jan '11

Hi all, >From what I understand it is only possible to have single line text inputs, i.e. <param type="text" size="10" ... Is it possible to have multiple line ones? e.g. user input line 1 includes newline user input line 2 etc. Did I miss something in the wiki? Cheers, Kostas

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persisting job_working_directory
by Darren Brown 26 Jan '11

26 Jan '11

Hello, I am building a tool for galaxy and am trying to debug it. I am using the latest central. When I run my tool I see a directory created under job_working_dir, containing my logs and such generated by my tool. However, this directory is deleted within a couple seconds of the job finishing. I have been searching for the config option to persist these working dirs but to no avail. I seem to find hints that these directories stick around for other folks. What am I missing? Thanks, Darren

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MySQL server has gone away error
by Marina Gourtovaia 26 Jan '11

26 Jan '11

Hello My Galaxy instance suffers from 'MySQL server has gone away error'. This error appears if the last web request was more than ~30-60 sec ago. The full traceback follows at the end of this message. If the same request is resent, everything is OK. My universe_wsgi.ini config file is set up as recommended for mysql. All timeouts on the database server itself are set well above 1min. This occurs both on etch and lenny Linux 64 bit nodes. The python version is 2.4 I would be helpful for any suggestions. Can move to postgresql, but rather stay with mysql. Marina Gourtovaia URL: http://sf-2-1-02.internal.sanger.ac.uk:9700/ File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py', line 97 in __call__ status, headers, body = wsgilib.intercept_output( File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 119 in __call__ trans = self.transaction_factory( environ ) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 161 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 181 in transaction_chooser return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 791 in __init__ self._ensure_valid_session( session_cookie ) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 318 in _ensure_valid_session self.app.model.GalaxySession.table.c.is_valid==True ) ) \ File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py', line 1300 in first ret = list(self[0:1]) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py', line 1221 in __getitem__ return list(res) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py', line 1361 in __iter__ return self._execute_and_instances(context) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py', line 1364 in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py', line 754 in execute return self.__connection(engine, close_with_result=True).execute( File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 824 in execute return Connection.executors[c](self, object, multiparams, params) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 874 in _execute_clauseelement return self.__execute_context(context) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 896 in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 950 in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['6683a26145119b72ce04fc6d4c6d7a0f', 1] -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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help with users and postgres
by Davide Cittaro 26 Jan '11

26 Jan '11

Dear all, Our local galaxy instance uses apache authentication to log users. This said, some users have no "User Name" and some other have a wrong "User name" (probably because they have been added before the apache integration). I just wonder if there's a way to modify the user names directly in the postgres database (I'm pretty sure that is possible...). Thanks d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Web API Key doc?
by Erick Antezana 26 Jan '11

26 Jan '11

Hi, where can I find some more info (examples) about the usage of the Galaxy Web API? thanks, Erick

2 1

quick question on tools' outputs...
by Kostas Karasavvas 26 Jan '11

26 Jan '11

Hi all! I have 2 outputs. During processing I catch some errors related to output2. Ideally, I would like to have in history the successful output as green and the failed output as red. Currently, the way I have implemented it, both history items are green but the second one contains the error. Is it possible to force a failure in selected outputs? Thank you, Kostas

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DevNewsBriefs?
by Davide Cittaro 25 Jan '11

25 Jan '11

There have been no DevNewsBriefs since the end of November... should I worry? :-) d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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