June 2012 - galaxy-dev - lists.galaxyproject.org

I can't see or access pictures in FastQC
by Dorset, Daniel C 07 Jun '12

07 Jun '12

I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files. If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named "dataset_###_files," and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct. Has anyone else experienced this problem?

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AttributeError: 'module' object has no attribute 'FakeSocket'
by Sarah Diehl 07 Jun '12

07 Jun '12

Hi all, today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/galaxy/galaxy_test/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/galaxy/galaxy_test/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/galaxy/galaxy_test/lib/galaxy/tools/__init__.py", line 33, in <module> from galaxy.util.shed_util import * File "/galaxy/galaxy_test/lib/galaxy/util/shed_util.py", line 14, in <module> from mercurial import ui, commands File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py", line 12, in <module> import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py", line 12, in <module> import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py", line 11, in <module> import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py", line 11, in <module> import changelog, byterange, url, error File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py", line 13, in <module> import httpconnection as httpconnectionmod File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py", line 16, in <module> from mercurial import httpclient File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py", line 48, in <module> import socketutil File "/galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py", line 82, in <module> class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket' Any help appreciated. Thanks. Sarah

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Galaxy server configuration question
by Huayan Gao 07 Jun '12

07 Jun '12

Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? Best, Huayan

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Load Balancer config doesn't work
by julie dubois 07 Jun '12

07 Jun '12

Hi, After several post in an Apache Forum, I've solve any problem of my apache configuration to enable load balancer configuration. It seems work but when I launch my galaxy application, I arrive in this web page : Service temporarily Unavailable And my log apache shows this : [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8083 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8082 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8081 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) [Tue May 29 09:37:32 2012] [error] (111)Connection refused: proxy: HTTP: attempt to connect to 127.0.0.1:8080 (localhost) failed [Tue May 29 09:37:32 2012] [error] ap_proxy_connect_backend disabling worker for (localhost) It means that galaxy doesn't listen the port 8080, 8081 ... I think it's my run.sh which cannot read my universe_wsgi.ini correctly. Because if it could read correctly, in my terminal I could see this type of line : Handling web0 with log file web0.log...Entering daemon mode... Now, Idon't see that! after the command GALAXY_RUN_ALL=1 sh run.sh --daemon, I just see : Entering Daemon mode. So in my view, it's not an Apache problem but a shell script galaxy problem. Somedy has already met this problem ? Have you a solution ? Thank you. Julie

2 1

Sharing data in Cistrome
by Päivi Pihlajamaa 07 Jun '12

07 Jun '12

Hi, I am trying to share my files/history in Galaxy/Cistrome with my colleague, but the 'Share with user' link gives the following error. Could you please help me, am i doing something wrong or is there a bug in the system? Best regards, Päivi Server Error URL: http://cistrome.org/ap/history/share?use_panels=False&id=7b2014ae6b4b7c3f Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:90 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.history:960 in share >> send_to_err=send_to_err ) Module galaxy.web.framework:733 in fill_template >> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako >> return template.render( **data ) Module mako.template:296 in render >> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _history_share_mako:74 in render_body >> __M_writer(unicode(history.name)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128) -- Päivi Pihlajamaa, M.Sc. Biomedicum Helsinki Institute of Biomedicine University of Helsinki phone +358-9-19125294 email paivi.pihlajamaa(a)helsinki.fi

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Incomplete datasets when dowloaded from history
by Jean-Francois Payotte 07 Jun '12

07 Jun '12

Hi folks, Some of our local Galaxy instance users seem to be experiencing some strange behaviour lately. I searched the mailing-list archive but I didn't found anything related, so I'd be interested to know if somebody already had the same issue. The problem is that sometimes, when people are trying to download their datasets from their history, although the file seems to download successfully, it appears that the downloaded file is incomplete (for example a 3000 lines text file will show only maybe 2000 lines at the first download, 1600 lines at the second download, and so on... and eventually, the file will download completely. This issue happened with more than one user and with different tools. Does anybody ever had this kind of issue? Or does somebody would have an idea of where to look to solve this problem? Best regards, Jean-François

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TopHat fusion
by suzan katie 07 Jun '12

07 Jun '12

Hello, Is there any plan of installing TopHat fusion in Galaxy in near future. Thanks Katie

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LookupError: No section 'main' (prefixed by 'server') found in config
by Iry Witham 07 Jun '12

07 Jun '12

I have performed a new install of Galaxy for development and deployment purposes. However, when I run the run.sh script I get the following error: Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 274, in command relative_to=base, global_conf=vars) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 308, in loadserver relative_to=relative_to, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 210, in loadserver return loadobj(SERVER, uri, name=name, **kw) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 363, in get_context object_type, name=name) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 528, in find_config_section self.filename)) LookupError: No section 'main' (prefixed by 'server') found in config /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini I have modified the universe_wsgi.ini to reflect the way our production server is configured. The following is the server section of that file: # # Galaxy is configured by default to be useable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: # # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer # # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. # examples of many of these options are explained in more detail in the wiki: # # Config hackers are encouraged to check there before asking for help. # ---- HTTP Server ---------------------------------------------------------- # Configuration of the internal HTTP server. [server:web0] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 2 [server:web1] use = egg:Paste#http port = 8081 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # Configuration of web server 3 [server:web2] use = egg:Paste#http port = 8082 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 # The internal HTTP server to use. Currently only Paste is provided. This # option is required. #use = egg:Paste#http # The port on which to listen. #port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. #use_threadpool = True # Number of threads in the web server thread pool. #threadpool_workers = 5 # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. # These filters are disabled by default. They can be enabled with # 'filter-with' in the [app:main] section below. # Define the gzip filter. [filter:gzip] use = egg:Paste#gzip # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy My production server works fine, but this one will not run. What am I missing? Thanks, Iry

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Group by c1: max[c2] --skipped 11489 invalid lines starting with line 3. Value '' in column 0 is not numeric
by Michael Thang 07 Jun '12

07 Jun '12

input file example in galaxy:WASH7P 0.305384KLHL17 6.4404GLTPD1 22.8633PUSL1 22.9327CPSF3L 0.446421SAMD11 0.0267019 output:AAAS then the error message complaint is on the tile column.After updating R to latest version the "grouping" function is no longer working. I have been searching very hard on the internet regarding to this issue. However, I have no luck to get any solution. This issue tracker is my last option by far. I have no idea what happened. thank

1 0

Is there a way to dynamically assign Queues in Galaxy
by Anthonius deBoer 06 Jun '12

06 Jun '12

Hi, I often find my self having to battle with other users of the cluster, even for the one-off jobs that someone runs interactively... We have setup Fast/short queues and Long queues... Is there a way for a tool to sometimes be placed in the fast queue and sometimes in the long queue? I know I can setup a tool in the universe file and add a -pe option there...But is there a way to dynamically assign jobs sometimes to one queue and sometimes to another? Even an option in the UI would work, since I could make the short queue the default for interactive work and people could turn it off in workflows that will run for a long time or will run with many samples.... Thanks Thon

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