- galaxy-dev - lists.galaxyproject.org

memdump
by Nikos Sidiropoulos 16 May '13

16 May '13

Hi everybody Has anybody used the "profile memory usage" feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos

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Re: [galaxy-dev] starting run_reports.sh fails
by Joachim Jacob | VIB | 16 May '13

16 May '13

No prob. Actually, I have found the answer thanks to the GalaxyAdmins meeting yesterday, where somebody extensively pointed to Trello ;-) Cheers J Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/15/2013 07:00 PM, Dannon Baker wrote: > Heh, thanks for answering both halves of the email before I could even > get to it :) > > > On Wed, May 15, 2013 at 12:03 PM, Joachim Jacob | VIB | > <joachim.jacob(a)vib.be <mailto:joachim.jacob@vib.be>> wrote: > > Already reported in Trello > https://trello.com/c/o0S3klAF > > Thanks for the fix! > > > Joachim Jacob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 <tel:%2B32%209%20244.66.34> > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote: > > run_reports.sh dies silently. > > Its last will in reports_webapp.log states: > > Traceback (most recent call last): > File "./scripts/paster.py", line 33, in <module> > serve.run() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 1056, in run > invoke(command, command_name, options, args[1:]) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 1062, in invoke > exit_code = runner.run(args) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 227, in run > result = self.command() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 650, in command > app = loadapp( app_spec, name=app_name, relative_to=base, > global_conf=vars) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 350, in loadapp > return loadobj(APP, uri, name=name, **kw) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 375, in loadobj > return context.create() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 813, in create > return self.object_type.invoke(self) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 249, in invoke > return fix_call(context.object, context.global_conf, > **context.local_conf) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 97, in fix_call > val = callable(*args, **kw) > File > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", > line 61, in app_factory > add_ui_controllers( webapp, app ) > File > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", > line 33, in add_ui_controllers > from galaxy.web.base.controller import BaseUIController > File > "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", > line 23, in <module> > from galaxy.visualization.genome.visual_analytics import > get_tool_def > File > "/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py", > line 3, in <module> > from galaxy.tools.parameters.basic import > IntegerToolParameter, FloatToolParameter, SelectToolParameter > File > "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line > 57, in <module> > from galaxy.visualization.genome.visual_analytics import > TracksterConfig > ImportError: cannot import name TracksterConfig > > Anybody knowing the recipe to reanimate the patient? Thanks. > BTW, this is the first time I am starting up run_reports.sh > after the 1 april/8 april update. Did not had this issue before. > > > Joachim > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >

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getaddrinfo() error on UCSC with Galaxy
by menorca chaturvedi 16 May '13

16 May '13

Hello, I am using UCSC to view mapped results on my local Galaxy. However, it shows this error: "getaddrinfo() error on hostName=...:Name or service not known. Couldn't open http://...." Any suggestions will be greatly appreciated. Best regards, Menorca

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getaddrinfo() error on UCSC with Galaxy
by Menorca Chaturvedi 16 May '13

16 May '13

Hello, I am using UCSC to view mapped results on my local Galaxy. However, it shows this error: "getaddrinfo() error on hostName=...:Name or service not known. Couldn't open http://...." Any suggestions will be greatly appreciated. Best regards, Menorca

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Web Page Problem
by sridhar srinivasan 16 May '13

16 May '13

Dear Developers, After installing galaxy, the history part of the webpage is not opening and it shows " Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem." when i try to reload in backend i am getting this message.. Exception happened during processing of request from ('192.168.1.6', 55016) Traceback (most recent call last): File "/illumina/apps/galaxy/galaxy-dist/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 618, in __init__ self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe Could anybody suggest on this issue... Thanks Sridhar

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Toolshed broken link
by Björn Grüning 15 May '13

15 May '13

Hi, if you are on the "manage tool dependencies" page the link to "get repository updates" is broken: ValueError: invalid literal for int() with base 10: 'b33e1f78e90a230d' Cheers, Björn

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adding a new ensemble genome build
by Nikolay N. 15 May '13

15 May '13

Hi, I am a galaxy newbie so apologise if the questions appears trivial. I installed an instance locally and would like to add the most recent Ensemble mouse genome build (http://www.ensembl.org/Mus_musculus/Info/Index) which is referred to using a confusing multitude of identifiers (this rant is not related to galaxy), among others GRCm38 (GCA_000001635.3), GRCm38.p1 and Ensemble mus musculis build 71. I wanted to add a record for this genome build in /home/nikolay/galaxy/galaxy-dist/tool-data/shared/ensembl/builds.txt. This file seems to have a tabular format and there are already some mouse records there: MGSC1 67 Mus_musculus (Mouse/MGSC1) MGSC3 67 Mus_musculus (Mouse/MGSC3) NCBIM30 67 Mus_musculus (Mouse/NCBIM30) NCBIM32 67 Mus_musculus (Mouse/NCBIM32) NCBIM33 67 Mus_musculus (Mouse/NCBIM33) NCBIM34 67 Mus_musculus (Mouse/NCBIM34) NCBIM35 67 Mus_musculus (Mouse/NCBIM35) NCBIM36 67 Mus_musculus (Mouse/NCBIM36) NCBIM37 67 Mus_musculus (Mouse/NCBIM37) But none of these records contains an id that bears any resemblance to the ids used by Ensemble. How do you guys come up with the ids for these genome builds? Is there any convention that I shall follow? Also, I find it a bit confusing that there is a numeric build id as well. It seems to be the same for all records. Does it have any role? (I assume not as it does not make sense to have the same id for all records). It would be really helpful if you can explain a bit more about the format/convention used in ensemble/builds.txt - if there is any. many thanks, Nick

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starting run_reports.sh fails
by Joachim Jacob | VIB | 15 May '13

15 May '13

run_reports.sh dies silently. Its last will in reports_webapp.log states: Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", line 61, in app_factory add_ui_controllers( webapp, app ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", line 33, in add_ui_controllers from galaxy.web.base.controller import BaseUIController File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 23, in <module> from galaxy.visualization.genome.visual_analytics import get_tool_def File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py", line 3, in <module> from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 57, in <module> from galaxy.visualization.genome.visual_analytics import TracksterConfig ImportError: cannot import name TracksterConfig Anybody knowing the recipe to reanimate the patient? Thanks. BTW, this is the first time I am starting up run_reports.sh after the 1 april/8 april update. Did not had this issue before. Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Imported datasets are marked as deleted
by pavan videm 15 May '13

15 May '13

Hi all, We have the following problem with importing datasets from data libraries. The datasets from data libraries can be imported in to the history but as soon as they imported they are marked as deleted. So I can see them only when 'Include Deleted Datasets' from history menu is ticked. There are no messages in the log files regarding this. One more observation is that in postgres database 'dataset' table, most of those datasets are already marked as deleted. I thought that somehow the cleanup scripts did that or? In which case this can happen? Could somebody please help me in debugging this issue? Thanks, Pavan

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report error
by Mónica Pérez Alegre 15 May '13

15 May '13

Good morning I would like if it´s arranged the floowing error: GURU MEDITATION: #9b1f321e13994a379d78c0b724b0e8b8 in my Galaxy Main session Thanks Kind regards

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