March 2010 - galaxy-dev - lists.galaxyproject.org

Feature request: highlight currently displayed history item.
by Pieter Neerincx 17 Mar '10

17 Mar '10

Hi Galaxy team, When working with histories with many items I sometimes get a little lost: which is the history item whose content is displayed in the middle section of my Galaxy window? (The output from different tools usually is different enough to prevent confusion, but when you process multiple samples in the same history it can get confusing.) Would it be possible to highlight the history item whose content is displayed in the center of a Galaxy window. Some other visual clue in middle section of a Galaxy window like a small heading or title bar with the name/tag of the displayed history item would probably also do the trick.... Cheers, Pi --------------------------------------------------------------- Biomolecular Mass Spectrometry & Proteomics group Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 6 143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ---------------------------------------------------------------

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Feature request: conf.d
by Pieter Neerincx 17 Mar '10

17 Mar '10

Hi Galaxy team, As my local instance grows it becomes more difficult each time to upgrade. I now use diff on the various config files to see what changes I should lift over to the new install. (I don't update, but leave my current setup untouched as a backup, create a new install and if that works switch to the new setup using a symlink.) Would it be possible to use a special directory with config files for site specific customizations? I'm thinking of something like Apache's "conf.d" directory or good ol' SRS's "sites" directory. This would allow us to leave the original Galaxy tools + datatypes config files untouched and list our local additions/mods in separate config files making upgrades a bit easier... Cheers, Pi --------------------------------------------------------------- Biomolecular Mass Spectrometry & Proteomics group Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 6 143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ---------------------------------------------------------------

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can no longer import data libraries into history
by Edward Kirton 16 Mar '10

16 Mar '10

please help! our install of galaxy is completely unable to load any data into libraries now! URL: http://galaxy.jgi-psf.org/library_common/act_on_multiple_datasets?library_i… File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/house/groupdirs/mep/galaxy/galaxy-dist/lib/galaxy/web/controllers/library_common.py', line 1384 in act_on_multiple_datasets archive.add( ldda.dataset.file_name, path ) UnboundLocalError: local variable 'archive' referenced before assignment i tried adding a new library to see if i could see it but i get an error symlinking or copying from filesystem paths: Miscellaneous information: Traceback (most recent call last): File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 326, in __main__() File "/house/groupdirs/mep/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in __main__ a error I could upload, but I still get the first error Thanks in advance for any assistance! Ed Kirton

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create multiple historie items
by vill 16 Mar '10

16 Mar '10

I have a perl script that splits a text file with genomic information (forward strand and reverse strand) in two separate files. One file for the forward strand and one file for the reverse strand. I have written a wrapper so that Galaxy can execute this script. When my script outputs one file this files is listed as a history item. When I let my script output the two files only one history item gets created. What I need to now is what extra variables do I need to output from the .xml file so that galaxy finds the two output files and puts both files in as a history item I have been looking at the "interval2maf .py and .xml" I just can't figure out how this works, it seems that the history_id is important and the species is a list array and for every species a file gets created in the databas/tmp directory and when the file is created the tmp dir is deleted. Adding and extra file from the .py into this tmp dir does not end up in the history items, renaming the files seems to end up with no history items at all. Cheers, //Michel

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Galaxy install error: NoSuchTableError: migrate_version
by Patrick T. 16 Mar '10

16 Mar '10

Hi, I've tried to install galaxy on my Ubuntu Linux amd64 2.6.27-11-generic, Python 2.5.2 (r252:60911), >>> sqlalchemy.__version__ '0.5.8', I ran $ hg clone http://bitbucket.org/galaxy/galaxy-central/ 5 days ago And I got this error after calling % sh run.sh Traceback (most recent call last): File "/home/tan/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/tan/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/home/tan/galaxy_dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database db_schema = schema.ControlledSchema( engine, migrate_repository ) File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 24, in __init__ self._load() File "/home/tan/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 36, in _load self.table = Table(tname, self.meta, autoload=True) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 110, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/var/lib/python-support/python2.5/sqlalchemy/schema.py", line 226, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/engine/base.py", line 1275, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py", line 343, in reflecttable raise exceptions.NoSuchTableError(table.name) NoSuchTableError: migrate_version /var/lib/python-support/python2.5/sqlalchemy/__init__ says ver 0.4.6 Thanks, Patrick __________________________________________________________________ Connect with friends from any web browser - no download required. Try the new Yahoo! Canada Messenger for the Web BETA at http://ca.messenger.yahoo.com/webmessengerpromo.php

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pre-set fields
by nsfox＠uwaterloo.ca 14 Mar '10

14 Mar '10

Hi, Is it possible to have textFields pre-set within a form or somewhere so that when someone goes and creates the sequence request certain fields are already set? Thanks, Natalie

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Re: [galaxy-dev] Database migration problem
by Jeremy Goecks 13 Mar '10

13 Mar '10

Hi Freerk, Can you be more specific about the problems that you're seeing? Also, please continue to cc galaxy-dev as you're more likely to get help with your issues since it's going to a larger audience. Thanks, J. On Mar 11, 2010, at 10:42 AM, Dijk, F van wrote: > Hi Jeremy, > > Thanks for the fast replay. The first issue is solved, a new one occured during the second point. When I migrate the sqlite database to SQL and try to import it into the MySQL database some errors occur. > MySQL is complaining about the syntax used in the SQLdump. > We are using the following MySQL version: > mysql Ver 14.12 Distrib 5.0.75, for debian-linux-gnu (x86_64) using readline 5.2 > I also read the info on the link you provided in your answer, but this won't solve this problem I think. So, do you have a solution? > > Sincerely, > > > Freerk van Dijk > > > Van: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] > Verzonden: donderdag 11 maart 2010 15:25 > Aan: Dijk, F van > CC: galaxy-dev(a)bx.psu.edu > Onderwerp: Re: [galaxy-dev] Database migration problem > > Hi Freerk, > >> When we change the databaseconnection to "mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock" in the universe_wsgi.ini file and run Galaxy we receive an error like: >> >> "Access denied for user 'root'@'localhost' (using password: NO)") None None >> >> So is there an option somewhere which we also have to change to make the connection work? >> > You need to specify a username and password to access your database. Try this URL: > > mysql://user:password@localhost/galaxy?unix_socket=/var/lib/mysql/mysql.sock > (exchanging 'user' and 'password' according to your settings) > >> And question two: >> Do we need to migrate the content from the sqlite database to the MySQL database by hand or does this happen automatically? >> > > You need to do the migration manually. Kanwei provided a nice solution to this problem a while back: > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-February/001996.html > > -- > What I would suggest is to dump the sqlite database to standard sql, > and then creating a new instance of galaxy that has mysql as the > configured database. When you run the setup and run script, you'll > have a freshly instantiated galaxy with empty mysql tables. Then you > can just import the standard sql file into the mysql database. > -- > > Good luck and let us know if you have any more problems. > > J. > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. >

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run.sh error
by Lin Jiang 11 Mar '10

11 Mar '10

Hi, I am trying to install galaxy in my macbook with python version 2.5.2. But I got error messages when I sh run.sh. Could you please help me with this? Best regards, Lin Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 218, in run result = self.command() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 313, in loadapp **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 413, in get_context section) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/Users/linjiang/galaxy_dist/lib/pkg_resources.py", line 1912, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/linjiang/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/Users/linjiang/galaxy_dist/lib/galaxy/web/framework/ __init__.py", line 29, in <module> from babel.support import Translations File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se

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run.sh error
by Lin Jiang 11 Mar '10

11 Mar '10

Hi, I am trying to install galaxy in my macbook with python version 2.5.2. But I got error messages when I sh run.sh. Could you please help me with this? Best regards, Lin Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/command.py", line 218, in run result = self.command() File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/Users/linjiang/galaxy_dist/eggs/PasteScript-1.7.3-py2.5.egg/ paste/script/serve.py", line 313, in loadapp **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 413, in get_context section) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/Users/linjiang/galaxy_dist/eggs/PasteDeploy-1.3.3-py2.5.egg/ paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/Users/linjiang/galaxy_dist/lib/pkg_resources.py", line 1912, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/linjiang/galaxy_dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, require_login, require_admin, url_for, error, form, FormBuilder File "/Users/linjiang/galaxy_dist/lib/galaxy/web/framework/ __init__.py", line 29, in <module> from babel.support import Translations File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/linjiang/galaxy_dist/eggs/Babel-0.9.4-py2.5.egg/babel/ core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' -- Lin Jiang, Ph.D student Dept. of Medical Biochemistry and Microbiology Uppsala University Husargatan 3 Biomedical Centre D11:3 307d Box 582 IMBIM Husdjursgenetik S-752 37 Uppsala Sweden Workphone: +46 (0) 18 471 4383 Lin.Jiang(a)imbim.uu.se

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Galaxy not finding DRMAA_python
by Chris Cole 11 Mar '10

11 Mar '10

Hi, We have two parallel installs of Galaxy one which runs with python2.4 and the other with 2.6. The 2.6 is working fine (other than the issues I've posted) however, the 2.4 won't start as it can't find DRMAA_python. I have scrambled the egg and it does exist: www-galaxy@ge-002: galaxy_live> ls -l /homes/www-galaxy/galaxy_live/eggs/DRMAA_python-0.2-py2.4-linux-x86_64-ucs4.egg -rw-r--r-- 1 www-galaxy barton 62374 Mar 5 14:22 /homes/www-galaxy/galaxy_live/eggs/DRMAA_python-0.2-py2.4-linux-x86_64-ucs4.egg What am I missing? Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

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