August 2013 - galaxy-dev - lists.galaxyproject.org

Galaxy Distribution Aug 12, 2013
by Jennifer Jackson 12 Aug '13

12 Aug '13

*Galaxy Distribution **Aug 12, 2013* / / /////http://bit.ly/galaxy20130812/ *Highlights:* * Upgrades to *Data Manager* including improved installation actions * *Visualization* Framework tunings, plus updates to *Phyloviz*, *Scatterplot*, and *Trackster *** * *Workflows* include new reproducibility controls and editing features * Multiple *Tool Shed* enhancements, features, and tunings * Plus additional updates to the *UI*, *Admin* and *Core*, and *API*, an important *Security Fix* reminder, and *Bug Fixes* http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.08.12 /Thanks for using Galaxy,/ The Galaxy Team -- Jennifer Hillman-Jackson http://galaxyproject.org

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Public production instance page is not loading properly with latest stable release
by Vipin TS 12 Aug '13

12 Aug '13

Hi Dev-team, I have updated my production instance to 10201:ebe87051fadf, The page is not loading properly. Please find the log message as following. serving on 0.0.0.0:8081 view at http://127.0.0.1:8080 X.X.X.X - - [12/Aug/2013:16:58:35 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" X.X.X.X - - [12/Aug/2013:16:58:36 -0400] "GET /root/welcome HTTP/1.1" 302 - "https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" X.X.X.X - - [12/Aug/2013:16:58:36 -0400] "GET /history HTTP/1.1" 200 - " https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" 66.249.72.219 - - [12/Aug/2013:17:00:02 -0400] "GET /history/delete_current?purge=True HTTP/1.1" 500 - "-" "Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'users_shared_with' URL: https://galaxy.cbio.mskcc.org/history/delete_current?purge=True File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/codebase/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/codebase/lib/galaxy/webapps/galaxy/controllers/history.py', line 540 in delete_current if history.users_shared_with: AttributeError: 'NoneType' object has no attribute 'users_shared_with' CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: '*/*' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_CONNECTION: 'Keep-Alive' HTTP_FROM: 'googlebot(at)googlebot.com' HTTP_HOST: 'galaxy.cbio.mskcc.org' HTTP_USER_AGENT: 'Mozilla/5.0 (compatible; Googlebot/2.1; + http://www.google.com/bot.html)' HTTP_X_FORWARDED_FOR: '66.249.72.219' HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org' HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org' HTTP_X_URL_SCHEME: 'https' ORGINAL_HTTP_HOST: 'localhost:8081' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history/delete_current' QUERY_STRING: 'purge=True' REMOTE_ADDR: '66.249.72.219' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x8c38850> is_api_request: False original_wsgi.url_scheme: 'http' paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x96d1dd0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x99e9f10> paste.parsed_querystring: ([('purge', 'True')], 'purge=True') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '28651434039211e389a390b11c087d99' webob._parsed_query_vars: (MultiDict([('purge', 'True')]), 'purge=True') wsgi process: 'Multithreaded' ------------------------------------------------------------ X.X.X.X - - [12/Aug/2013:17:00:42 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) rekonq Safari/534.34" Is that something missing here, Thanks V ipin

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How can I shorten refresh time?
by Ramon Tiburski 12 Aug '13

12 Aug '13

When I run some tool or some workflow, delay about 2 or 3 seconds to refresh the page, where can I change it? Thank you...

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[GSoC2013] Week 7 and Week 8 Update
by Saket Choudhary 12 Aug '13

12 Aug '13

Hi Everyone, Here is an update for the last 2 weeks: http://galaxy-gsoc2013.blogspot.com/2013/08/week-7-and-week-8-update.html Saket

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Adding GATK tools to Galaxy Cloudman
by Iry Witham 12 Aug '13

12 Aug '13

Hi Team, I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Error at initialization of module heapycTraceback / Last sources of Galaxy
by Sarah Maman 12 Aug '13

12 Aug '13

Dear all, When I try to install last sources of Galaxy(% hg clone https://bitbucket.org/galaxy/galaxy-dist/) , I have this error : Error at initialization of module heapycTraceback (most recent call last): File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/lib/galaxy/app.py", line 157, in __init__ self.memdump = memdump.Memdump() File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/lib/galaxy/util/memdump.py", line 24, in __init__ self.heapy = guppy.hpy() File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/__init__.py", line 35, in hpy return r.guppy.heapy.Use File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 202, in getattr2 x = self.getattr_package(inter, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 250, in getattr_package x = self.makeModule(x, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 310, in makeModule return Share(module, self, module.__name__, Clamp) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 176, in __init__ getattr(inter, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 204, in getattr2 x = self.getattr3(inter, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 272, in getattr3 pa = getattr(pa, at) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 202, in getattr2 x = self.getattr_package(inter, name) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 239, in getattr_package x = __import__(self.makeName(name), globals(), locals()) File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/heapy/View.py", line 556, in <module> prime_builtin_types() File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/heapy/View.py", line 539, in prime_builtin_types import guppy.heapy.heapyc File "/usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/sets/__init__.py", line 3, in <module> from setsc import BitSet # base bitset type ImportError: /usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/sets/setsc.so: undefined symbol: _PyLong_AsScaledDouble Coul you please help me ? Thanks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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Quoted paths in universe_wsgi.ini - configuration error?
by Peter Cock 12 Aug '13

12 Aug '13

Hello all, While trying to install the Glimmer3 wrapper from the Tool Shed I noticed some very wrong looking paths, including this warning at the terminal where run.sh was open, Warning: local() encountered an error (return code 1) while executing 'echo 'PYTHONPATH=$PYTHONPATH:/opt/galaxy-dist/"../galaxy-dist-shed-tools"/biopython/1.61/biopython/package_biopython_1_61/5d0c54f7fea2/lib/python; export PYTHONPATH' > '/opt/galaxy-dist/"../galaxy-dist-shed-tools"/biopython/1.61/bgruening/glimmer3/ab12adaa5cc2/env.sh';chmod +x '/opt/galaxy-dist/"../galaxy-dist-shed-tools"/biopython/1.61/bgruening/glimmer3/ab12adaa5cc2/env.sh'' >From my configuration file, $ grep tool_dependency_dir universe_wsgi.ini tool_dependency_dir = "../galaxy-dist-shed-tools" Installation of the dependencies failed. I removed the quotes in the tool_dependency_dir setting, restarted Galaxy, uninstalled Glimmer3 and the Biopython dependency, and then re-installed Glimmer3. This time the paths in the terminal looked sensible, although there was still a warning: Warning: local() encountered an error (return code 255) while executing 'export PYTHONPATH=$PYTHONPATH:/opt/galaxy-dist-shed-tools/biopython/1.61/biopython/package_biopython_1_61/5d0c54f7fea2/lib/python && I think that is related to the currently broken dependency issue I mentioned here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015971.html I would expect Galaxy to strip the quotes (after all, they are commonly used to escape filenames with spaces). Perhaps it is but doing so inconsistently? It appears Python's path checking is a bit odd here: $ python Python 2.7.2 (default, Aug 6 2013, 16:54:30) [GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import os >>> p = '../galaxy-dist-shed-tools' >>> q = '"../galaxy-dist-shed-tools"' >>> os.path.isfile(p) False >>> os.path.isfile(q) False >>> os.path.join(os.path.curdir, p) './../galaxy-dist-shed-tools' >>> os.path.join(os.path.curdir, q) './"../galaxy-dist-shed-tools"' >>> os.path.isdir(os.path.join(os.path.curdir, p)) True >>> os.path.isdir(os.path.join(os.path.curdir, q)) True >>> os.path.abspath(p) '/opt/galaxy-dist-shed-tools' >>> os.path.abspath(q) '/opt/galaxy-dist/"../galaxy-dist-shed-tools"' >>> os.path.isdir(os.path.abspath(p)) True >>> os.path.isdir(os.path.abspath(q)) True >>> quit() This feels like a bug in the Python os module to me? Anyway, a quick hack to fix this would be to strip the quotes when loading file or path names from the configuration file - or abort with a clear error telling the user to remove them? Peter

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How to send a file from galaxy to an external URL
by Delphine LARIVIERE 12 Aug '13

12 Aug '13

Dear Galaxy developers, I am a beginner in galaxy development and I would like to build a tool to send a file from galaxy to an external URL. I tried to work with the following tutorial : http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications… But I couldn't make it work and it doesn't seem to fit exactly to what I want to do. I would be grateful if you could help me with this issue, Thank you everyone, Delphine -- Delphine Larivière Ph.D Student in Bioinformatics CIRAD Data Integration Team email: delphine.lariviere(a)cirad.fr

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cummerBund installation
by sridhar srinivasan 12 Aug '13

12 Aug '13

Dear Developers, Could you please tell me the possibilities of using the R package cummeRband for visualization of RNA-seq data in galaxy?? Thanks Sridhar

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Help with installation
by Jurgens de Bruin 12 Aug '13

12 Aug '13

To all, I am getting the following error when I run sh run.sh : galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 51, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 318, in __new__ table._init(name, metadata, *args, **kw) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 381, in _init self._autoload(metadata, autoload_with, include_columns) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py", line 408, in _autoload self, include_columns, exclude_columns File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2425, in run_callable return conn.run_callable(callable_, *args, **kwargs) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1968, in run_callable return callable_(self, *args, **kwargs) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 260, in reflecttable return insp.reflecttable(table, include_columns, exclude_columns) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 370, in reflecttable for col_d in self.get_columns(table_name, schema, **tblkw): File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 223, in get_columns **kw) File "<string>", line 1, in <lambda> File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py", line 47, in cache ret = fn(self, con, *args, **kw) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py", line 713, in get_columns (pragma, qtable))) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1628, in _execute_text statement, parameters File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) disk I/O error u'PRAGMA table_info("dataset")' () Please any help would be appreciated!! -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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