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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 --*--

2 1

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

1 0

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

1 0

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

3 2

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

3 3

Problems with Tophat & uploading files to Cloudman by FTP
by Anto Praveen Rajkumar Rajamani 11 Aug '13

11 Aug '13

Hello, I started a new cloudman instance two days ago. I am stuck with two problems. 1. When I try to upload my fastq files to FTP server using Filezilla (I typed my ec2... address as the host and entered my cloudman registered email address and password), Filezilla connects to 220-Galaxy Cloudman FTP but then rejects my password and displays "Could not connect to server". I could see some command line based suggestions in this forum (http://dev.list.galaxyproject.org/Connecting-to-new-Galaxy-Cloudman-by-FTP-…) but I do not know how to employ them. 2. When I try tophat on my pilot data, Cloudman fails and gives a message, "Could not determine Tophat version /mnt/galaxy/tmp/job_working_directory/000/30/galaxy_30.sh: 13: /mnt/galaxy/tmp/job_working_directory/000/30/galaxy_30.sh: tophat: not found /bin/sh: 1: tophat: not found Error indexing reference sequence /bin/sh: 1: bow" I repeated running tophat many times without any success. I tried uploading fastq files to my Google drive and provided the file download url to the upload file tool. It did not work. Kindly help me to come out of these problems. Thanking you in advance. Best wishes, Anto

1 1

Fwd: Public production instance page is not rendering properly
by Vipin TS 09 Aug '13

09 Aug '13

--/Vipin ---------- Forwarded message ---------- From: Vipin TS <vipin.ts(a)gmail.com> Date: Fri, Aug 9, 2013 at 5:04 PM Subject: Re: [galaxy-dev] Public production instance page is not rendering properly To: Daniel Blankenberg <dan(a)bx.psu.edu> Hi Dan, Thanks for your support, Hmm, I can see that there are changes: but here is the out come from the below commands: $$ hg diff templates/webapps/galaxy/root/history.mako empty $$ hg summary parent: 10218:ff0bd4a811d9 tip merged the changes from stable release version July 2013 from bx.psu.edu branch: default commit: 5 modified, 5 removed, 452 deleted update: 1663 new changesets, 2 branch heads (merge) $$hg config Sorry, it says unknown option. Do you think I have mixed up something ? Thank you, Vipin On Fri, Aug 9, 2013 at 4:41 PM, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: > Hi Vipin, > > Strange, are you running the latest galaxy-dist? That line doesn't exist > in e.g. > https://bitbucket.org/galaxy/galaxy-dist/src/ebe87051fadff5750ec226490b31e4…. > Can you compare your file to the file in the repository? What is the output > of: > > hg diff templates/webapps/galaxy/root/history.mako > > and > > hg summary > > and > > hg config > > > > > Thanks for using Galaxy, > > Dan > > On Aug 9, 2013, at 3:56 PM, Vipin TS wrote: > > Hi Dan, > > I deleted the > contents from > /codebase/database/complied_templates/* and restarted the instance, still > no luck. Sorry. > > Thanks, Vipin > > > On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: > >> Hi Vipin, >> >> Can you try deleting the contents of your compiled templates directory >> (i.e. >> /codebase/database/compiled_templates/*)? >> >> Thanks for using Galaxy, >> >> Dan >> >> >> On Aug 9, 2013, at 3:22 PM, Vipin TS wrote: >> >> Hi Dan, >> >> Thanks for the information, I have updated this to my repository >> manually. Now I can invoke the page but the frames were not loaded >> correctly. >> >> The log message as follows: >> /codebase/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: >> SAWarning: The IN-predicate on "request_type.id" was invoked with an >> empty sequence. This results in a contradiction, which nonetheless can be >> expensive to evaluate. Consider alternative strategies for improved >> performance. >> X.X.X.X - - [09/Aug/2013:15:09:55 -0400] "GET / HTTP/1.1" 200 - "-" >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.26.17 >> (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /root/tool_menu HTTP/1.1" >> 404 - "https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (Macintosh; Intel >> Mac OS X 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /history HTTP/1.1" 200 - " >> https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> X.X.X.X - - [09/Aug/2013:15:09:56 -0400] "GET /history HTTP/1.1" 500 - " >> https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10_7_5) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 >> Safari/536.26.17" >> ---------------------------------------- >> Exception happened during processing of request from ('127.0.0.1', 43370) >> Traceback (most recent call last): >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 1068, in process_request_in_thread >> self.finish_request(request, client_address) >> File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request >> self.RequestHandlerClass(request, client_address, self) >> File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__ >> self.handle() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 442, in handle >> BaseHTTPRequestHandler.handle(self) >> File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle >> self.handle_one_request() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 437, in handle_one_request >> self.wsgi_execute() >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line >> 287, in wsgi_execute >> self.wsgi_start_response) >> File "/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py", line >> 203, in __call__ >> return app(environ, start_response) >> File "/codebase/lib/galaxy/web/framework/middleware/request_id.py", >> line 12, in __call__ >> return self.app( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py", >> line 21, in __call__ >> return self.app( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", >> line 68, in __call__ >> return self.application(environ, replacement_start_response) >> File "/codebase/lib/galaxy/web/framework/middleware/error.py", line >> 159, in __call__ >> exc_info) >> File "/codebase/lib/galaxy/web/framework/middleware/translogger.py", >> line 67, in replacement_start_response >> return start_response( status, headers, exc_info ) >> 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 199, in >> handle_request >> return body( environ, start_response ) >> File "/codebase/lib/galaxy/web/framework/__init__.py", line 985, in >> render >> template.render_context( context ) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py", line 319, >> in render_context >> **kwargs) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 692, >> in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) >> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 718, >> in _exec_template >> callable_(context, *args, **kwargs) >> File "/codebase/database/compiled_templates/root/history.mako.py", >> line 73, in render_body >> if bool( [ data for data in history.active_datasets if data.state in >> ['running', 'queued', '', None ] ] ): >> AttributeError: 'Undefined' object has no attribute 'active_datasets' >> >> Do you have any quick way to fix the same? Or update to galaxy-central >> stable branch? >> >> Thank you, Vipin >> >> On Fri, Aug 9, 2013 at 2:57 PM, Daniel Blankenberg <dan(a)bx.psu.edu>wrote: >> >>> Hi Vipin, >>> >>> This has been fixed in the stable branch of galaxy-central >>> https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but >>> has not made it on to galaxy-dist yet. >>> >>> >>> Thanks for using Galaxy, >>> >>> Dan >>> >>> >>> >>> On Aug 9, 2013, at 2:33 PM, Vipin TS wrote: >>> >>> Hello dev-team, >>> >>> I am experiencing a strange problem with my production instance, after I >>> carefully merged remote changes from galaxy-dist release to my code >>> repository. While restarting, It fails to load the the page properly, the >>> message from log file stating that "serving on 0.0.0.0:8080" >>> >>> Here are some message found in the log file: >>> >>> X.X.X.X - - [09/Aug/2013:14:30:56 -0400] "GET / HTTP/1.1" 500 - "-" >>> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) >>> rekonq Safari/534.34" >>> Error - <type 'exceptions.ValueError'>: expected only letters, got ' en' >>> URL: https://galaxy.cbio.mskcc.org/ >>> 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 159 in >>> handle_request >>> trans = self.transaction_factory( environ ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in >>> <lambda> >>> self.set_transaction_factory( lambda e: self.transaction_chooser( e, >>> galaxy_app, session_cookie ) ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in >>> transaction_chooser >>> return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie >>> ) >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in >>> __init__ >>> self.setup_i18n() >>> File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in >>> setup_i18n >>> locales.append( Locale.parse( locale.split( ';' )[0], sep='-' >>> ).language ) >>> File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in >>> parse >>> return cls(*parse_locale(identifier, sep=sep)) >>> File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in >>> parse_locale >>> raise ValueError('expected only letters, got %r' % lang) >>> ValueError: expected only letters, got ' en' >>> >>> >>> CGI Variables >>> ------------- >>> CONTENT_LENGTH: '0' >>> HTTP_ACCEPT: >>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' >>> HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5' >>> HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate' >>> HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6' >>> HTTP_CACHE_CONTROL: 'max-age=0' >>> HTTP_CONNECTION: 'Keep-Alive' >>> HTTP_HOST: 'galaxy.cbio.mskcc.org' >>> HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 >>> (KHTML, like Gecko) rekonq Safari/534.34' >>> HTTP_X_FORWARDED_FOR: '172.21.50.129' >>> 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: '/' >>> REMOTE_ADDR: '172.21.50.129' >>> 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 0x7f78910> >>> is_api_request: False >>> original_wsgi.url_scheme: 'http' >>> paste.expected_exceptions: [<class >>> 'paste.httpexceptions.HTTPException'>] >>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler >>> object at 0x7f78210> >>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at >>> 0x8066d90> >>> 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: 'd4f643a8012111e3819090b11c087d99' >>> wsgi process: 'Multithreaded' >>> ------------------------------------------------------------ >>> >>> Any idea what is going wrong here? Please let me know if you need more >>> get more details. >>> >>> Many thanks, >>> --/Vipin >>> >>> ___________________________________________________________ >>> 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/ >>> >>> >>> >> >> > >

1 1

Public production instance page is not rendering properly
by Vipin TS 09 Aug '13

09 Aug '13

Hello dev-team, I am experiencing a strange problem with my production instance, after I carefully merged remote changes from galaxy-dist release to my code repository. While restarting, It fails to load the the page properly, the message from log file stating that "serving on 0.0.0.0:8080" Here are some message found in the log file: X.X.X.X - - [09/Aug/2013:14:30:56 -0400] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) rekonq Safari/534.34" Error - <type 'exceptions.ValueError'>: expected only letters, got ' en' URL: https://galaxy.cbio.mskcc.org/ 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 159 in handle_request trans = self.transaction_factory( environ ) File '/codebase/lib/galaxy/web/framework/__init__.py', line 238 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/codebase/lib/galaxy/web/framework/__init__.py', line 269 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/codebase/lib/galaxy/web/framework/__init__.py', line 332 in __init__ self.setup_i18n() File '/codebase/lib/galaxy/web/framework/__init__.py', line 370 in setup_i18n locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language ) File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse return cls(*parse_locale(identifier, sep=sep)) File '/codebase/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 763 in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got ' en' CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'utf-8,*;q=0.5' HTTP_ACCEPT_ENCODING: 'gzip, deflate, x-gzip, x-deflate' HTTP_ACCEPT_LANGUAGE: 'en-US, en-US; q=0.8, en; q=0.6' HTTP_CACHE_CONTROL: 'max-age=0' HTTP_CONNECTION: 'Keep-Alive' HTTP_HOST: 'galaxy.cbio.mskcc.org' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) rekonq Safari/534.34' HTTP_X_FORWARDED_FOR: '172.21.50.129' 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: '/' REMOTE_ADDR: '172.21.50.129' 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 0x7f78910> is_api_request: False original_wsgi.url_scheme: 'http' paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f78210> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x8066d90> 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: 'd4f643a8012111e3819090b11c087d99' wsgi process: 'Multithreaded' ------------------------------------------------------------ Any idea what is going wrong here? Please let me know if you need more get more details. Many thanks, --/Vipin

2 5

Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)
by Rodolfo Aramayo 09 Aug '13

09 Aug '13

Hi, Regarding the error I experienced with [galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable) Two things: FIRST The error I reported, in short, it was my fault as I failed to to set up the: cmdline = '/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' line properly in the oases_optimiser.py script properly I guess it would help for developers to state exactly the customization required for each package installed via ToolShed for the tool to work properly or better yet, it would be really nice if we could set up environmental variables like: TOOL_SHED_REPOS=/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu… so that scripts could invoke them upon installation: cmdline = '$TOOL_SHED_REPOS/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' SECOND I still am experiencing errors with this tool When I run oases_optimiser on either fasta or fastq files the jobs start, run and then fail In all cases the problem is the lack of an ''splicing_events.txt' file Help will be appreciated Thanks --R ##### The stderr is as follows: Traceback (most recent call last): File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 120, in <module> if __name__ == "__main__": __main__() File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 76, in __main__ for line in open(path ): IOError: [Errno 2] No such file or directory: 'splicing_events.txt' ##### The stdout is as follows: [0.000000] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [13.354877] 8855297 sequences found [13.354879] Done [13.354940] Reading read set file ./Sequences; [14.405160] 8855297 sequences found [20.956147] Done [20.956153] 8855297 sequences in total. [20.956229] Writing into roadmap file ./Roadmaps... [23.008558] Inputting sequences... [23.008571] Inputting sequence 0 / 8855297 [25.835351] Inputting sequence 1000000 / 8855297 [28.835964] Inputting sequence 2000000 / 8855297 [31.938277] Inputting sequence 3000000 / 8855297 [35.129436] Inputting sequence 4000000 / 8855297 [38.384093] Inputting sequence 5000000 / 8855297 [41.660153] Inputting sequence 6000000 / 8855297 [44.905326] Inputting sequence 7000000 / 8855297 [48.168615] Inputting sequence 8000000 / 8855297 [50.969068] === Sequences loaded in 28.188442 s [50.969101] Done inputting sequences [50.969103] Destroying splay table [51.018112] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [13.140830] 8855297 roadmaps read [13.144978] Creating insertion markers [15.796233] Ordering insertion markers [21.652798] Counting preNodes [22.631404] 2753107 preNodes counted, creating them now [24.516794] Sequence 1000000 / 8855297 [25.609456] Sequence 2000000 / 8855297 [26.585862] Sequence 3000000 / 8855297 [27.501523] Sequence 4000000 / 8855297 [28.375045] Sequence 5000000 / 8855297 [29.217391] Sequence 6000000 / 8855297 [30.037355] Sequence 7000000 / 8855297 [30.838062] Sequence 8000000 / 8855297 [31.514315] Adjusting marker info... [32.498044] Connecting preNodes [32.734023] Connecting 1000000 / 8855297 [33.029694] Connecting 2000000 / 8855297 [33.360000] Connecting 3000000 / 8855297 [33.712200] Connecting 4000000 / 8855297 [34.080947] Connecting 5000000 / 8855297 [34.464629] Connecting 6000000 / 8855297 [34.853754] Connecting 7000000 / 8855297 [35.256476] Connecting 8000000 / 8855297 [35.604610] Cleaning up memory [35.622205] Done creating preGraph [35.622208] Concatenation... [36.944164] Renumbering preNodes [36.944174] Initial preNode count 2753107 [36.992738] Destroyed 2139761 preNodes [36.992745] Concatenation over! [36.992747] Clipping short tips off preGraph [37.241017] Concatenation... [37.561728] Renumbering preNodes [37.561735] Initial preNode count 613346 [37.564816] Destroyed 602327 preNodes [37.564818] Concatenation over! [37.564819] 565869 tips cut off [37.564820] 11019 nodes left [37.564908] Writing into pregraph file ./PreGraph... [37.628994] Reading read set file ./Sequences; [38.666026] 8855297 sequences found [45.262765] Done [47.287358] Reading pre-graph file ./PreGraph [47.287449] Graph has 11019 nodes and 8855297 sequences [47.320337] Scanning pre-graph file ./PreGraph for k-mers [47.345965] 587492 kmers found [47.410094] Sorting kmer occurence table ... [47.807351] Sorting done. [47.807356] Computing acceleration table... [47.839961] Computing offsets... [47.856571] Ghost Threading through reads 0 / 8855297 [49.327252] Ghost Threading through reads 1000000 / 8855297 [50.789941] Ghost Threading through reads 2000000 / 8855297 [52.251861] Ghost Threading through reads 3000000 / 8855297 [53.719122] Ghost Threading through reads 4000000 / 8855297 [55.175811] Ghost Threading through reads 5000000 / 8855297 [56.640149] Ghost Threading through reads 6000000 / 8855297 [58.103628] Ghost Threading through reads 7000000 / 8855297 [59.570354] Ghost Threading through reads 8000000 / 8855297 [60.865193] === Ghost-Threaded in 13.008623 s [60.865203] Threading through reads 0 / 8855297 [62.545417] Threading through reads 1000000 / 8855297 [64.224281] Threading through reads 2000000 / 8855297 [65.912903] Threading through reads 3000000 / 8855297 [67.591620] Threading through reads 4000000 / 8855297 [69.271917] Threading through reads 5000000 / 8855297 [70.956665] Threading through reads 6000000 / 8855297 [72.633673] Threading through reads 7000000 / 8855297 [74.323969] Threading through reads 8000000 / 8855297 [75.752202] === Threaded in 14.886999 s [76.213422] Correcting graph with cutoff 0.200000 [76.215727] Determining eligible starting points [76.223605] Done listing starting nodes [76.223606] Initializing todo lists [76.224193] Done with initilization [76.224195] Activating arc lookup table [76.224796] Done activating arc lookup table [76.246815] 10000 / 11019 nodes visited [76.247077] Concatenation... [76.247364] Renumbering nodes [76.247365] Initial node count 11019 [76.247654] Removed 140 null nodes [76.247655] Concatenation over! [76.247655] Clipping short tips off graph, drastic [76.251632] Concatenation... [76.363538] Renumbering nodes [76.363546] Initial node count 10879 [76.363860] Removed 3988 null nodes [76.363861] Concatenation over! [76.363862] 6891 nodes left [76.363931] Writing into graph file ./Graph2... [77.954766] WARNING: NO COVERAGE CUTOFF PROVIDED [77.954770] Velvet will probably leave behind many detectable errors [77.954771] See manual for instructions on how to set the coverage cutoff parameter [77.954779] Removing contigs with coverage < -1.000000... [77.959164] Concatenation... [77.959591] Renumbering nodes [77.959591] Initial node count 6891 [77.959603] Removed 0 null nodes [77.959604] Concatenation over! [77.959817] Concatenation... [77.959947] Renumbering nodes [77.959947] Initial node count 6891 [77.959958] Removed 0 null nodes [77.959958] Concatenation over! [77.959962] Clipping short tips off graph, drastic [77.960338] Concatenation... [77.960467] Renumbering nodes [77.960468] Initial node count 6891 [77.960479] Removed 0 null nodes [77.960479] Concatenation over! [77.960479] 6891 nodes left [77.960481] WARNING: NO EXPECTED COVERAGE PROVIDED [77.960481] Velvet will be unable to resolve any repeats [77.960481] See manual for instructions on how to set the expected coverage parameter [77.960482] Concatenation... [77.960610] Renumbering nodes [77.960610] Initial node count 6891 [77.960621] Removed 0 null nodes [77.960621] Concatenation over! [77.960622] Removing reference contigs with coverage < -1.000000... [77.960918] Concatenation... [77.961047] Renumbering nodes [77.961047] Initial node count 6891 [77.961058] Removed 0 null nodes [77.961059] Concatenation over! [78.028474] Writing contigs into ./contigs.fa... [79.423669] Writing into stats file ./stats.txt... [79.559581] Writing into graph file ./LastGraph... Final graph has 6891 nodes and n50 of 96, max 2769, total 569496, using 5202858/8855297 reads [0.000000] Reading graph file ./Graph2 [0.000070] Graph has 6891 nodes and 8855297 sequences [2.414712] Reading read set file ./Sequences; [3.454420] 8855297 sequences found [9.983101] Done [12.073890] Removing contigs with coverage < 3.000000... [12.077227] Concatenation... [12.110841] Renumbering nodes [12.110844] Initial node count 6891 [12.111045] Removed 112 null nodes [12.111046] Concatenation over! [12.111295] Concatenation... [12.111423] Renumbering nodes [12.111423] Initial node count 6779 [12.111436] Removed 0 null nodes [12.111436] Concatenation over! [12.111441] Clipping short tips off graph, drastic [12.112174] Concatenation... [12.112311] Renumbering nodes [12.112312] Initial node count 6779 [12.112405] Removed 7 null nodes [12.112406] Concatenation over! [12.112406] 6772 nodes left [12.112407] Correcting graph with cutoff 0.200000 [12.112413] Removing low coverage edges from the graph [12.116981] Concatenation... [12.205746] Renumbering nodes [12.205752] Initial node count 6772 [12.205956] Removed 32 null nodes [12.205957] Concatenation over! [12.206236] Determining eligible starting points [12.209874] Done listing starting nodes [12.209876] Initializing todo lists [12.210092] Done with initilization [12.210092] Activating arc lookup table [12.210256] Done activating arc lookup table [12.211125] 1000 nodes visited [12.211314] 2000 nodes visited [12.211725] 3000 nodes visited [12.211981] 4000 nodes visited [12.212184] 5000 nodes visited [12.212412] 6000 nodes visited [12.212988] 7000 nodes visited [12.214581] 8000 nodes visited [12.214905] 9000 nodes visited [12.215178] 10000 nodes visited [12.215483] 11000 nodes visited [12.215855] 12000 nodes visited [12.216435] 13000 nodes visited [12.217246] Concatenation... [12.239617] Renumbering nodes [12.239620] Initial node count 6740 [12.239808] Removed 78 null nodes [12.239809] Concatenation over! [12.239810] Clipping short tips off graph, drastic [12.240542] Concatenation... [12.269659] Renumbering nodes [12.269667] Initial node count 6662 [12.269860] Removed 21 null nodes [12.269861] Concatenation over! [12.269861] 6641 nodes left [12.269863] Removing low coverage edges from the graph [12.270134] Concatenation... [12.270253] Renumbering nodes [12.270254] Initial node count 6641 [12.270266] Removed 0 null nodes [12.270267] Concatenation over! [12.270750] Writing into stats file ./stats.txt... [12.418659] Writing into graph file ./LastGraph... Computing local connections [18.310196] Activating arc lookup table [18.310878] Done activating arc lookup table Extracting loci from connection graph... [18.532657] Counted 3577 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [18.623163] Exporting transcripts to ./transcripts.fa [18.637751] Exporting transcript contigs to ./contig-ordering.txt [18.773863] Finished extracting transcripts, used 4747390/8855297 reads [0.000000] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [12.768650] 8855297 sequences found [12.768653] Done [12.945838] Reading read set file ./Sequences; [13.863345] 8855297 sequences found [19.497520] Done [19.497531] 8855297 sequences in total. [19.541544] Writing into roadmap file ./Roadmaps... [21.360277] Inputting sequences... [21.360288] Inputting sequence 0 / 8855297 [23.204556] Inputting sequence 1000000 / 8855297 [25.109676] Inputting sequence 2000000 / 8855297 [27.073594] Inputting sequence 3000000 / 8855297 [29.074912] Inputting sequence 4000000 / 8855297 [31.101859] Inputting sequence 5000000 / 8855297 [33.295043] Inputting sequence 6000000 / 8855297 [35.624233] Inputting sequence 7000000 / 8855297 [37.969184] Inputting sequence 8000000 / 8855297 [39.983558] === Sequences loaded in 18.844462 s [40.106935] Done inputting sequences [40.106938] Destroying splay table [40.147227] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [10.688511] 8855297 roadmaps read [10.694034] Creating insertion markers [12.646929] Ordering insertion markers [16.397709] Counting preNodes [17.105913] 1802122 preNodes counted, creating them now [18.580180] Sequence 1000000 / 8855297 [19.551491] Sequence 2000000 / 8855297 [20.443988] Sequence 3000000 / 8855297 [21.288288] Sequence 4000000 / 8855297 [22.100638] Sequence 5000000 / 8855297 [22.889490] Sequence 6000000 / 8855297 [23.659644] Sequence 7000000 / 8855297 [24.414121] Sequence 8000000 / 8855297 [25.053583] Adjusting marker info... [25.710606] Connecting preNodes [25.814606] Connecting 1000000 / 8855297 [25.936316] Connecting 2000000 / 8855297 [26.072741] Connecting 3000000 / 8855297 [26.215108] Connecting 4000000 / 8855297 [26.368631] Connecting 5000000 / 8855297 [26.522818] Connecting 6000000 / 8855297 [26.681469] Connecting 7000000 / 8855297 [26.845782] Connecting 8000000 / 8855297 [26.987872] Cleaning up memory [27.003705] Done creating preGraph [27.003708] Concatenation... [27.767289] Renumbering preNodes [27.767294] Initial preNode count 1802122 [27.793408] Destroyed 1115129 preNodes [27.793419] Concatenation over! [27.793421] Clipping short tips off preGraph [27.933941] Concatenation... [27.943271] Renumbering preNodes [27.943273] Initial preNode count 686993 [27.946796] Destroyed 685336 preNodes [27.946798] Concatenation over! [27.946799] 676719 tips cut off [27.946799] 1657 nodes left [27.946865] Writing into pregraph file ./PreGraph... [27.958115] Reading read set file ./Sequences; [29.008103] 8855297 sequences found [35.730429] Done [37.535139] Reading pre-graph file ./PreGraph [37.750964] Graph has 1657 nodes and 8855297 sequences [37.755970] Scanning pre-graph file ./PreGraph for k-mers [37.774919] 85345 kmers found [37.784901] Sorting kmer occurence table ... [37.821440] Sorting done. [37.821442] Computing acceleration table... [37.839000] Computing offsets... [37.841254] Ghost Threading through reads 0 / 8855297 [38.725065] Ghost Threading through reads 1000000 / 8855297 [39.601268] Ghost Threading through reads 2000000 / 8855297 [40.473358] Ghost Threading through reads 3000000 / 8855297 [41.347286] Ghost Threading through reads 4000000 / 8855297 [42.220368] Ghost Threading through reads 5000000 / 8855297 [43.096893] Ghost Threading through reads 6000000 / 8855297 [43.969893] Ghost Threading through reads 7000000 / 8855297 [44.844439] Ghost Threading through reads 8000000 / 8855297 [45.596543] === Ghost-Threaded in 7.755290 s [45.596549] Threading through reads 0 / 8855297 [46.518374] Threading through reads 1000000 / 8855297 [47.444445] Threading through reads 2000000 / 8855297 [48.366937] Threading through reads 3000000 / 8855297 [49.288411] Threading through reads 4000000 / 8855297 [50.211439] Threading through reads 5000000 / 8855297 [51.138604] Threading through reads 6000000 / 8855297 [52.061485] Threading through reads 7000000 / 8855297 [52.985071] Threading through reads 8000000 / 8855297 [53.776191] === Threaded in 8.179642 s [54.119435] Correcting graph with cutoff 0.200000 [54.119719] Determining eligible starting points [54.120670] Done listing starting nodes [54.120672] Initializing todo lists [54.120754] Done with initilization [54.120755] Activating arc lookup table [54.120825] Done activating arc lookup table [54.123725] Concatenation... [54.123766] Renumbering nodes [54.123766] Initial node count 1657 [54.123811] Removed 12 null nodes [54.123812] Concatenation over! [54.123813] Clipping short tips off graph, drastic [54.124252] Concatenation... [54.224979] Renumbering nodes [54.224989] Initial node count 1645 [54.225027] Removed 685 null nodes [54.225028] Concatenation over! [54.225029] 960 nodes left [54.225116] Writing into graph file ./Graph2... [55.367296] WARNING: NO COVERAGE CUTOFF PROVIDED [55.367299] Velvet will probably leave behind many detectable errors [55.367299] See manual for instructions on how to set the coverage cutoff parameter [55.367310] Removing contigs with coverage < -1.000000... [55.369762] Concatenation... [55.369800] Renumbering nodes [55.369800] Initial node count 960 [55.369804] Removed 0 null nodes [55.369804] Concatenation over! [55.369836] Concatenation... [55.369852] Renumbering nodes [55.369852] Initial node count 960 [55.369854] Removed 0 null nodes [55.369855] Concatenation over! [55.369859] Clipping short tips off graph, drastic [55.369917] Concatenation... [55.369933] Renumbering nodes [55.369933] Initial node count 960 [55.369935] Removed 0 null nodes [55.369936] Concatenation over! [55.369936] 960 nodes left [55.369937] WARNING: NO EXPECTED COVERAGE PROVIDED [55.369938] Velvet will be unable to resolve any repeats [55.369938] See manual for instructions on how to set the expected coverage parameter [55.369939] Concatenation... [55.369955] Renumbering nodes [55.369955] Initial node count 960 [55.369957] Removed 0 null nodes [55.369958] Concatenation over! [55.369958] Removing reference contigs with coverage < -1.000000... [55.370004] Concatenation... [55.370020] Renumbering nodes [55.370020] Initial node count 960 [55.370023] Removed 0 null nodes [55.370023] Concatenation over! [55.422086] Writing contigs into ./contigs.fa... [56.445270] Writing into stats file ./stats.txt... [56.509837] Writing into graph file ./LastGraph... Final graph has 960 nodes and n50 of 97, max 2466, total 83275, using 3349500/8855297 reads [0.000000] Reading graph file ./Graph2 [0.000036] Graph has 960 nodes and 8855297 sequences [1.504128] Reading read set file ./Sequences; [2.507512] 8855297 sequences found [9.014853] Done [11.103883] Removing contigs with coverage < 3.000000... [11.106359] Concatenation... [11.106391] Renumbering nodes [11.106392] Initial node count 960 [11.106405] Removed 0 null nodes [11.106406] Concatenation over! [11.106437] Concatenation... [11.106451] Renumbering nodes [11.106452] Initial node count 960 [11.106454] Removed 0 null nodes [11.106454] Concatenation over! [11.106457] Clipping short tips off graph, drastic [11.106511] Concatenation... [11.106526] Renumbering nodes [11.106526] Initial node count 960 [11.106528] Removed 0 null nodes [11.106529] Concatenation over! [11.106529] 960 nodes left [11.106530] Correcting graph with cutoff 0.200000 [11.106533] Removing low coverage edges from the graph [11.107536] Concatenation... [11.143393] Renumbering nodes [11.143395] Initial node count 960 [11.143419] Removed 2 null nodes [11.143420] Concatenation over! [11.143472] Determining eligible starting points [11.143963] Done listing starting nodes [11.143965] Initializing todo lists [11.143992] Done with initilization [11.143993] Activating arc lookup table [11.144018] Done activating arc lookup table [11.144227] 1000 nodes visited [11.144573] Concatenation... [11.170620] Renumbering nodes [11.170625] Initial node count 958 [11.170649] Removed 3 null nodes [11.170650] Concatenation over! [11.170650] Clipping short tips off graph, drastic [11.170755] Concatenation... [11.170770] Renumbering nodes [11.170770] Initial node count 955 [11.170777] Removed 1 null nodes [11.170777] Concatenation over! [11.170778] 954 nodes left [11.170778] Removing low coverage edges from the graph [11.170807] Concatenation... [11.170821] Renumbering nodes [11.170822] Initial node count 954 [11.170824] Removed 0 null nodes [11.170825] Concatenation over! [11.170964] Writing into stats file ./stats.txt... [11.230812] Writing into graph file ./LastGraph... Computing local connections [14.746804] Activating arc lookup table [14.746902] Done activating arc lookup table Extracting loci from connection graph... [14.901713] Counted 680 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [14.943051] Exporting transcripts to ./transcripts.fa [14.945550] Exporting transcript contigs to ./contig-ordering.txt [15.018696] Finished extracting transcripts, used 2812567/8855297 reads [0.000000] Reading FastA file transcripts_19.fa; [0.010226] 1570 sequences found [0.010227] Done [0.010247] Reading FastA file transcripts_21.fa; [0.011900] 344 sequences found [0.011901] Done [0.011933] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [12.198483] 8855297 sequences found [12.198486] Done [12.401859] Reading read set file ./Sequences; [13.230828] 8857211 sequences found [18.721759] Done [18.721771] 8857211 sequences in total. [18.757685] Writing into roadmap file ./Roadmaps... [20.584822] Inputting sequences... [20.584833] Inputting sequence 0 / 8857211 [22.366728] Inputting sequence 1000000 / 8857211 [24.064109] Inputting sequence 2000000 / 8857211 [25.810546] Inputting sequence 3000000 / 8857211 [27.594079] Inputting sequence 4000000 / 8857211 [29.489010] Inputting sequence 5000000 / 8857211 [31.550585] Inputting sequence 6000000 / 8857211 [33.630592] Inputting sequence 7000000 / 8857211 [35.727077] Inputting sequence 8000000 / 8857211 [37.556610] === Sequences loaded in 17.186429 s [37.658648] Done inputting sequences [37.658651] Destroying splay table [37.699062] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [9.685475] 8857211 roadmaps read [9.691067] Creating insertion markers [10.875179] Ordering insertion markers [15.994335] Counting preNodes [16.591386] 1819394 preNodes counted, creating them now [18.120056] Sequence 1000000 / 8857211 [19.096796] Sequence 2000000 / 8857211 [20.019315] Sequence 3000000 / 8857211 [20.903522] Sequence 4000000 / 8857211 [21.760984] Sequence 5000000 / 8857211 [22.597284] Sequence 6000000 / 8857211 [23.416069] Sequence 7000000 / 8857211 [24.216209] Sequence 8000000 / 8857211 [24.899732] Adjusting marker info... [25.431336] Connecting preNodes [25.558999] Connecting 1000000 / 8857211 [25.675256] Connecting 2000000 / 8857211 [25.804199] Connecting 3000000 / 8857211 [25.937344] Connecting 4000000 / 8857211 [26.076245] Connecting 5000000 / 8857211 [26.221485] Connecting 6000000 / 8857211 [26.374118] Connecting 7000000 / 8857211 [26.527566] Connecting 8000000 / 8857211 [26.663482] Cleaning up memory [26.676121] Done creating preGraph [26.676124] Concatenation... [27.334684] Renumbering preNodes [27.334691] Initial preNode count 1819394 [27.360193] Destroyed 1162378 preNodes [27.360203] Concatenation over! [27.360204] Clipping short tips off preGraph [27.472827] Concatenation... [27.482889] Renumbering preNodes [27.482890] Initial preNode count 657016 [27.486213] Destroyed 654610 preNodes [27.486215] Concatenation over! [27.486215] 642103 tips cut off [27.486216] 2406 nodes left [27.486304] Writing into pregraph file ./PreGraph... [27.632873] Reading read set file ./Sequences; [28.652946] 8857211 sequences found [35.138336] Done [36.942242] Reading pre-graph file ./PreGraph [37.162349] Graph has 2406 nodes and 8857211 sequences [37.177742] Scanning pre-graph file ./PreGraph for k-mers [37.202831] 323188 kmers found [37.235987] Sorting kmer occurence table ... [37.412622] Sorting done. [37.412631] Computing acceleration table... [37.436981] Computing offsets... [37.446554] Ghost Threading through reads 0 / 8857211 [38.426036] Ghost Threading through reads 1000000 / 8857211 [39.403194] Ghost Threading through reads 2000000 / 8857211 [40.382459] Ghost Threading through reads 3000000 / 8857211 [41.359848] Ghost Threading through reads 4000000 / 8857211 [42.338263] Ghost Threading through reads 5000000 / 8857211 [43.312651] Ghost Threading through reads 6000000 / 8857211 [44.288659] Ghost Threading through reads 7000000 / 8857211 [45.262101] Ghost Threading through reads 8000000 / 8857211 [46.097808] === Ghost-Threaded in 8.651254 s [46.097819] Threading through reads 0 / 8857211 [47.257090] Threading through reads 1000000 / 8857211 [48.297172] Threading through reads 2000000 / 8857211 [49.336488] Threading through reads 3000000 / 8857211 [50.376047] Threading through reads 4000000 / 8857211 [51.415893] Threading through reads 5000000 / 8857211 [52.455649] Threading through reads 6000000 / 8857211 [53.494621] Threading through reads 7000000 / 8857211 [54.534154] Threading through reads 8000000 / 8857211 [55.426228] === Threaded in 9.328408 s [55.878521] Correcting graph with cutoff 0.200000 [55.878882] Determining eligible starting points [55.880237] Done listing starting nodes [55.880238] Initializing todo lists [55.880345] Done with initilization [55.880346] Activating arc lookup table [55.880433] Done activating arc lookup table [55.882259] Concatenation... [55.882315] Renumbering nodes [55.882316] Initial node count 2406 [55.882381] Removed 8 null nodes [55.882391] Concatenation over! [55.882391] Clipping short tips off graph, drastic [55.883006] Concatenation... [55.986679] Renumbering nodes [55.986689] Initial node count 2398 [55.986751] Removed 757 null nodes [55.986752] Concatenation over! [55.986753] 1641 nodes left [55.986847] Writing into graph file ./Graph2... [57.586219] WARNING: NO COVERAGE CUTOFF PROVIDED [57.586222] Velvet will probably leave behind many detectable errors [57.586223] See manual for instructions on how to set the coverage cutoff parameter [57.586229] Removing contigs with coverage < -1.000000... [57.588755] Concatenation... [57.588822] Renumbering nodes [57.588823] Initial node count 1641 [57.588828] Removed 0 null nodes [57.588828] Concatenation over! [57.588882] Concatenation... [57.588910] Renumbering nodes [57.588910] Initial node count 1641 [57.588914] Removed 0 null nodes [57.588914] Concatenation over! [57.588918] Clipping short tips off graph, drastic [57.589010] Concatenation... [57.589038] Renumbering nodes [57.589038] Initial node count 1641 [57.589042] Removed 0 null nodes [57.589042] Concatenation over! [57.589043] 1641 nodes left [57.589044] WARNING: NO EXPECTED COVERAGE PROVIDED [57.589044] Velvet will be unable to resolve any repeats [57.589045] See manual for instructions on how to set the expected coverage parameter [57.589046] Concatenation... [57.589073] Renumbering nodes [57.589074] Initial node count 1641 [57.589077] Removed 0 null nodes [57.589077] Concatenation over! [57.589078] Removing reference contigs with coverage < -1.000000... [57.589313] Concatenation... [57.589342] Renumbering nodes [57.589343] Initial node count 1641 [57.589346] Removed 0 null nodes [57.589347] Concatenation over! [57.642005] Writing contigs into ./contigs.fa... [59.115401] Writing into stats file ./stats.txt... [59.194880] Writing into graph file ./LastGraph... Final graph has 1641 nodes and n50 of 253, max 2780, total 321253, using 4663132/8857211 reads [0.000000] Reading graph file ./Graph2 [0.000035] Graph has 1641 nodes and 8857211 sequences [2.107753] Reading read set file ./Sequences; [3.038393] 8857211 sequences found [9.441180] Done [11.533317] Removing contigs with coverage < 3.000000... [11.536633] Concatenation... [11.536765] Renumbering nodes [11.536766] Initial node count 1641 [11.536809] Removed 38 null nodes [11.536810] Concatenation over! [11.536862] Concatenation... [11.536889] Renumbering nodes [11.536889] Initial node count 1603 [11.536892] Removed 0 null nodes [11.536893] Concatenation over! [11.536896] Clipping short tips off graph, drastic [11.536986] Concatenation... [11.537012] Renumbering nodes [11.537013] Initial node count 1603 [11.537016] Removed 0 null nodes [11.537017] Concatenation over! [11.537017] 1603 nodes left [11.537018] Correcting graph with cutoff 0.200000 [11.537021] Removing low coverage edges from the graph [11.537755] Concatenation... [11.570878] Renumbering nodes [11.570880] Initial node count 1603 [11.570922] Removed 2 null nodes [11.570923] Concatenation over! [11.570992] Determining eligible starting points [11.571857] Done listing starting nodes [11.571859] Initializing todo lists [11.571906] Done with initilization [11.571907] Activating arc lookup table [11.571953] Done activating arc lookup table [11.572158] 1000 nodes visited [11.572367] 2000 nodes visited [11.572720] 3000 nodes visited [11.574751] Concatenation... [11.658520] Renumbering nodes [11.658526] Initial node count 1601 [11.658573] Removed 13 null nodes [11.658575] Concatenation over! [11.658576] Clipping short tips off graph, drastic [11.658669] Concatenation... [11.658696] Renumbering nodes [11.658696] Initial node count 1588 [11.658699] Removed 0 null nodes [11.658700] Concatenation over! [11.658700] 1588 nodes left [11.658701] Removing low coverage edges from the graph [11.658754] Concatenation... [11.658779] Renumbering nodes [11.658779] Initial node count 1588 [11.658783] Removed 0 null nodes [11.658783] Concatenation over! [11.659006] Writing into stats file ./stats.txt... [11.739723] Writing into graph file ./LastGraph... Computing local connections [16.410447] Activating arc lookup table [16.410585] Done activating arc lookup table Extracting loci from connection graph... [16.589680] Counted 1507 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [16.653772] Exporting transcripts to ./transcripts.fa [16.668614] Exporting transcript contigs to ./contig-ordering.txt [16.783990] Finished extracting transcripts, used 4672425/8857211 reads [16.787745] Printing unused reads into ./UnusedReads.fa [24.411594] Writing into AMOS file ./oases_asm.afg... Thanks Again --R

1 0

One small problem for experts, one giant question for me..
by Can Holyavkin 09 Aug '13

09 Aug '13

Hello everyone, Firstly, I am beginner. I am a new Galaxy user that installed the Galaxy locally into my ubuntu (13.04) installed computer. Everything is working perfectly right now. Galaxy is really awesome. To learn the basics, I started the basic tutorial (Galaxy101 https://main.g2.bx.psu.edu/u/aun1/p/galaxy101) that helps too much. This tutorial consist a step for explaning "Compare Two Datasets" function. I did exactly everthing the instructor said however that module become red in History with following error: tool error An error occured with dataset: Unable to finish job (screenshot of error: http://i.imgur.com/xHqhK72.png) I wrote the bug report at end of the mail. Interestingly, when I press "View" button, I get the data that I wanted. However, any metadata is seen. So I can not see the final results on the UCSC browser. I replicate the same module at public server, it didn't gave an error. What might cause this kind of problem? Does reinstalling solve this problem? Would you please help me? Thank you everyone. Traceback (most recent call last): File "/home/can/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 94, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/can/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009, in finish self.sa_session.flush() File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE job SET update_time=?, stdout=?, stderr=? WHERE job.id = ?' ('2013-08-09 09:00:48.464260', 'join (GNU coreutils) 8.20\nCopyright (C) 2012 Free Software Foundation, Inc.\nLisans GPLv3+: GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1 <http://gnu.org/licenses/gpl.html>.\nBu \xc3\x96zg\xc3\xbcr bir yaz\xc4\xb1l\xc4\xb1md\xc4\xb1r: de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f\xc4\xb1tmakta \xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4\xb1n izin verdi\xc4\x9fi \xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir GARANT\xc4\xb0 sunulmaz.\n\nMike Haertel taraf\xc4\xb1ndan yaz\xc4\xb1ld\xc4\xb1.\n', '', 41) Can Holyavkin PhD Student Istanbul Technical University Molecular Biology and Genetics Dept.

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