- galaxy-dev - lists.galaxyproject.org

tool_sheds_errors
by Wang, Xiaofei 13 Mar '14

13 Mar '14

Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! ________________________________ From: Greg Von Kuster [greg(a)bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Hello, It's difficult to determine the cause of the problem in your environment based on the details you've provided. If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there. If you see them installed elsewhere, then that setting must have been set differently at the time they were installed. You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them. Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them. If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, "Wang, Xiaofei" <xfwang(a)ku.edu<mailto:xfwang@ku.edu>> wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing". Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/<http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies>Tool<http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies>%20Dependencies<http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies> #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! ------------------------------------------------------------------------------------------ Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster ___________________________________________________________ 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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Re: [galaxy-dev] Local Galaxy web layout
by sam guerler 13 Mar '14

13 Mar '14

Hi Shenwiyn, Can you specify what is not working? Did you find the file? Thanks, Sam On Wed, Feb 19, 2014 at 1:42 AM, shenwiyn(a)gmail.com <shenwiyn(a)gmail.com>wrote: > Hi Sam and Hans-Rudolf， > Thank you very much for your help.It seems that the > static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a > result,would you please show me some more details about this? > > Regards, Shenwiyn > > > *From:* sam guerler <aysam.guerler(a)gmail.com> > *Date:* 2014-02-18 01:20 > *To:* Hans-Rudolf Hotz <hrh(a)fmi.ch> > *CC:* shenwiyn(a)gmail.com; galaxy-dev <galaxy-dev(a)lists.bx.psu.edu> > *Subject:* Re: [galaxy-dev] Local Galaxy web layout > Hi Shenwiyn, > > This has changed recently. Please take a look at: > > static/scripts/galaxy.menu.js > > Using that file, you can add/remove/change labels and their position. It > is recommended to run pack_scripts.py after changing the source file. > > Regards, Sam > > > On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: > >> Hi Shenwiyn >> >> >> Have a look at: >> >> ~/galaxy_dist/database/compiled_templates/base_panels.mako.py >> >> >> Regards, Hans-Rudolf >> >> >> >> >> On 02/17/2014 08:04 AM, shenwiyn(a)gmail.com wrote: >> >>> Galaxy developers: >>> I want to change my local Galaxy web layout,for example,delete the top >>> button of "Visualization" and "Cloud" or change their positions.Could >>> anyone show me some details about this? >>> Thank you very much. >>> >>> ------------------------------------------------------------------------ >>> shenwiyn(a)gmail.com >>> >>> >>> ___________________________________________________________ >>> 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/ >>> >>> ___________________________________________________________ >> 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/ >> > >

3 2

tool_dependency_dir (Installed, missing tool dependencies)
by Wang, Xiaofei 13 Mar '14

13 Mar '14

Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this " set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing". Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin "manage installed tool shed repositories", the installation status is "Installed, missing tool dependencies" for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread "The migrated BWA installed but missing dependencies". But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! ------------------------------------------------------------------------------------------ Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster

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installed bwa but there are no bwa files produced in galaxy-dist folder
by Anna 13 Mar '14

13 Mar '14

Hello guys, I've got a problem with the integration of the BWA Tool in Galaxy. I installed BWA and Galaxy in a virtual box and now I want integrate BWA as a tool. For this I have to do this steps: $ sudo cp /home/ubuntu/galaxy-dist/bwa-0.7.4/bwa /usr/local/bin now bwa can be run from the command line $ bwa The Galaxy tool also requires a loc file which contains the locations of indexes for locally stored genome builds. We don't have any so we can just use the empty sample: $ cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc $ sh run.sh --reload The problem is, that in my tool-data folder doesn't exist bwa files even if bwa is installed and aso linked in the bin folder! I hope you can help me, because I don't know what to do now! Thanks and greets, Anna

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Re: [galaxy-dev] Plugins
by Michael E. Cotterell 12 Mar '14

12 Mar '14

Over next couple days, I'll take a look at what's in lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it with my stuff in order to get a general plugin framework (galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a math class this semester is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/ On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote: > It is web-specific and only handles the mako/static serving cases. I think the only areas we were generalizing at this point were the directory structures and main configuration. > > Agreed on more generalization and the hook system. Michael's stuff is a good direction to move in. > > I know John was looking to use it for dynamic job destinations and dynamic toolbox filters. I'd like to see some lab/community discussion on (even broad stroke) functional requirements and use cases. > > > On Tue, Sep 3, 2013 at 12:27 PM, James Taylor <james(a)jamestaylor.org (mailto:james@jamestaylor.org)> wrote: > > Carl, is what you have now totally web specific? It would be great to > > have a general plugin framework (galaxy.pluginframework) which the web > > stuff could perhaps extend? > > > > > > On Tue, Sep 3, 2013 at 10:56 AM, Carl Eberhard <carlfeberhard(a)gmail.com (mailto:carlfeberhard@gmail.com)> wrote: > > > Heya, Michael > > > > > > Right now our only plugin code is located in > > > lib/galaxy/web/base/pluginframework.py. It's only purpose so far is to: > > > - allow locally modified/created code to serve mako templates and static > > > pages/resources from paste. > > > - serve as a super class for the visualization framework. > > > > > > I think your git repo has some great ideas. > > > > > > Carl > > > > > > > > > On Fri, Aug 30, 2013 at 2:25 PM, Michael Cotterell <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)> > > > wrote: > > > > > > > > Is this plugin code hosted anywhere (like in central)? > > > > > > > > > > > > On Monday, August 26, 2013, James Taylor wrote: > > > > > > > > > > Michael, > > > > > > > > > > Carl has been working on a plugin framework for Galaxy, and John > > > > > Chilton has made some improvements. It would be great if you could > > > > > look over what each other has done and come up with some suggestions. > > > > > I personally am in favor of a very generic hook system where a hook > > > > > can be defined anywhere in the code and then the user can provide any > > > > > callable. > > > > > > > > > > I'm fond of the way sup implemented hooks, see the use of HookManager > > > > > here: https://github.com/sup-heliotrope/sup/blob/develop/lib/sup/time.rb > > > > > > > > > > Your approach is quite similar and I like it. > > > > > > > > > > This makes it easy to have a script that can list all available hooks > > > > > with their documentation. > > > > > > > > > > > > > > > -- > > > > > James Taylor, Assistant Professor, Biology/CS, Emory University > > > > > > > > > > > > > > > On Fri, Aug 23, 2013 at 10:29 AM, Michael E. Cotterell > > > > > <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com)> wrote: > > > > > > James, > > > > > > > > > > > > Has there been any more talk about this? I'd be willing to work in my > > > > > > reference implementation into central as a pull request, but I don't want to > > > > > > do that unless there is an agreed upon roadmap or something. > > > > > > > > > > > > Thanks! > > > > > > > > > > > > Sincerely, > > > > > > Michael E. Cotterell > > > > > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > > > Instructor of Record, Graduate RA & TA, University of Georgia > > > > > > Department Liaison, CS Graduate Student Association, University of > > > > > > Georgia > > > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com) > > > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) (mailto:mepcott@uga.edu) > > > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) (mailto:mec@cs.uga.edu) > > > > > > http://michaelcotterell.com/ > > > > > > > > > > > > > > > > > > On Tuesday, July 16, 2013 at 2:08 PM, Michael E. Cotterell wrote: > > > > > > > > > > > > > James, > > > > > > > > > > > > > > That's exactly what I was thinking. In my opinion, hooks are the way > > > > > > > to go (as seen in my example), but if there's a better way then I'm game for > > > > > > > that to. I just want to be able to extend Galaxy without modifying Galaxy > > > > > > > itself. > > > > > > > > > > > > > > Thanks! > > > > > > > > > > > > > > Sincerely, > > > > > > > Michael E. Cotterell > > > > > > > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > > > > Instructor of Record, Graduate RA & TA, University of Georgia > > > > > > > Faculty Liaison, CS Graduate Student Association, University of > > > > > > > Georgia > > > > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com) > > > > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) (mailto:mepcott@uga.edu) > > > > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) (mailto:mec@cs.uga.edu) > > > > > > > http://michaelcotterell.com/ > > > > > > > > > > > > > > > > > > > > > On Tuesday, July 16, 2013 at 2:05 PM, James Taylor wrote: > > > > > > > > > > > > > > > Michael, > > > > > > > > > > > > > > > > Galaxy is all about plugins! Tools, datatypes, batch systems, > > > > > > > > visualizations, et cetera. > > > > > > > > > > > > > > > > Additional ways to extend Galaxy through plugins are very welcome. > > > > > > > > We > > > > > > > > just need to make sure that whatever solution is chosen is extremely > > > > > > > > general. > > > > > > > > > > > > > > > > -- > > > > > > > > James Taylor, Assistant Professor, Biology/CS, Emory University > > > > > > > > > > > > > > > > > > > > > > > > On Tue, Jul 16, 2013 at 1:57 PM, Michael E. Cotterell > > > > > > > > <mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) (mailto:mepcotterell@gmail.com)> wrote: > > > > > > > > > Are there any plans in the works to support plugins within Galaxy? > > > > > > > > > One of the tools I'm working on is actually more of an extension of the > > > > > > > > > workflow canvas/editor's user interface. Right now, I've minimized the > > > > > > > > > modifications required to the editor.mako file to simply adding a mako > > > > > > > > > include near the bottom of the file. However, like I just said, this > > > > > > > > > requires editing a Galaxy file. It would be a lot better if Galaxy supported > > > > > > > > > plugins with hooks, thus allowing me to extend the user interface (or any > > > > > > > > > other part of the application) by registering hooks in a plugin. > > > > > > > > > > > > > > > > > > To demonstrate how easy it would be to integrate plugins into a > > > > > > > > > python application, I've written up a simple plugin manager script (~100 > > > > > > > > > loc) an placed it in a gist: https://gist.git > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Sincerely, > > > > Michael E. Cotterell > > > > > > > > Ph.D. Student in Computer Science, University of Georgia > > > > Graduate RA & TA, University of Georgia > > > > mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) > > > > mepcott(a)uga.edu (mailto:mepcott@uga.edu) > > > > mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) > > > > http://michaelcotterell.com/ > > > > > >

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Write permission for database/files
by Kucukural, Alper 12 Mar '14

12 Mar '14

Hi All, Galaxy opens a directory under database/files when the #of data files increased. So, it goes 1,2,3 … etc. I want to give a write permission for these specific directories when they are created without changing umask in the user profile. Is there anybody who can tell me where galaxy creates these directories. Thanks in advance. Best, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: Alper.Kucukural(a)umassmed.edu

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History seems to load forever
by Ganote, Carrie L 12 Mar '14

12 Mar '14

Hi List, I just pulled and merged from galaxy-dist (I think it's dc067a95261d), updated my database, and migrated my tools. The issues I am able to see are minor, but I have a user who can no longer access a particular history. It apparently just hangs. If they delete the history, Galaxy responds, but it will hang again when they try to add back any datasets. Unfortunately, I don't see any errors in the paster logs about this. I fear that their dataset entries in the Postgresql db have been corrupted during the update, or perhaps the files themselves were purged. I cannot reproduce their issues with my own histories - I'm able to bring up saved histories and upload etc. I don't know if they can share a history if it can't be loaded. How should I troubleshoot this? I'm set up to authenticate through apache, which makes it harder to get in as the user and see what's up. Is there an easy way to find out what histories belong to what users? I can search the database? Any advice would be greatly appreciated! -Carrie

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nginx upload -> traceback
by Langhorst, Brad 12 Mar '14

12 Mar '14

I’ve been trying to get the nxinx upload stuff working… I think i have the nginx config is working properly (files are present in the right spot with correct ownership and have correct content), but I see a traceback in the log (see below). I don’t see anything in the mail list search about this, so maybe I’ve done something wrong... — here’s are the relevant bits of my galaxy config file --- # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. # Configuration for this is complex and explained in detail in the # documentation linked above. The upload store is a temporary directory in # which files uploaded by the upload module will be placed. nginx_upload_store = /mnt/galaxy/data/galaxy/tmp/upload_store # This value overrides the action set on the file upload form, e.g. the web # path where the nginx_upload_module has been configured to intercept upload # requests. nginx_upload_path = /_upload ——nginx config —— #direct file uploads location /_upload { upload_store /mnt/galaxy/data/galaxy/tmp/upload_store; upload_pass_form_field ""; upload_set_form_field "__${upload_field_name}__is_composite" "true"; upload_set_form_field "__${upload_field_name}__keys" "name path"; upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; upload_pass_args on; upload_pass /_upload_done; } location /_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; } Any ideas? Brad File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 92 in __call__ return self.app( environ, start_response ) File '/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 84 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 1869 in handle_input self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {}, source=source ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2263 in update_state current_case = input.get_current_case( value, trans ) File '/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 462 in get_current_case raise Exception( "No case matched value:", self.name, str_value ) Exception: ('No case matched value:', 'files_metadata', None) CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'multipart/form-data; boundary=----WebKitFormBoundaryfTsa16a7MJyYSF0i' HTTP_ACCEPT: 'application/json' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_AUTHORIZATION: 'Basic bGFuZ2hvcnN0Om1pZWRoaWRsc2hhZmRv' HTTP_CACHE_CONTROL: 'no-cache' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be; __utma=171448127.504006193.1380078797.1392 167382.1394500277.13; __utmc=171448127; __utmz=171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/' HTTP_DNT: '1' HTTP_HOST: 'galaxy.neb.com<http://galaxy.neb.com>' HTTP_ORIGIN: 'http://galaxy.neb.com' HTTP_REFERER: 'http://galaxy.neb.com/' HTTP_REMOTE_USER: 'langhorst(a)neb.com<mailto:langhorst@neb.com>' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.117 Safari/537.36' HTTP_X_FORWARDED_FOR: '172.17.1.252' HTTP_X_FORWARDED_HOST: 'galaxy.neb.com<http://galaxy.neb.com>' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' ORGINAL_HTTP_HOST: 'galaxy_app' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/tool_runner/index' REMOTE_ADDR: '172.17.1.252' REQUEST_METHOD: 'POST' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x98d8cd0> is_api_request: False paste.cookies: (<SimpleCookie: __utma='171448127.504006193.1380078797.1392167382.1394500277.13' __utmc='171448127' __utmz='171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/' galaxysession='dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be'>, 'galaxysession=dacacca08a0d5b7ec42fdebd408f7de21fe616408da7cc0a81d03a170f28a8adb286af52e48220be; __utma=171448127.504006193.1380078797.1392167382.1394500277.13; __utmc=171448127; __utmz=171448127.1392167382.12.5.utmcsr=duckduckgo.com<http://duckduckgo.com>|utmccn=(referral)|utmcmd=referral|utmcct=/') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x98d8ad0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x9c3ed50> 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: '6193e9a2a9db11e388e10050568436c1' webob._parsed_post_vars: (MultiDict([('history_id', '792704c2cfd232ef'), ('tool_id', 'upload1'), ('inputs', '{"dbkey":"?","file_type":"auto","files_0|type":"upload_dataset","files_0|url_paste":"","space_to_tabs":false}'), ('__files_0|file_data__is_composite', 'true'), ('__files_0|file_data__keys', 'name path'), ('files_0|file_data_name', 'seq_elements2.txt'), ('files_0|file_data_path', '/mnt/galaxy/data/galaxy/tmp/upload_store/0000000004')]), <FakeCGIBody at 7f4f001a8c90 viewing MultiDict([('hi...4')])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

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job_wrapper.finish - No JSON object could be decoded:
by Peter Cock 12 Mar '14

12 Mar '14

Hi all, Some of our split BLAST jobs using the parallelism feature have been failing (apparently for a while, so this is not a recent problem from changes in the BLAST wrappers) as follows: <quote> The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/runners/tasks.py", line 141, in queue_job job_wrapper.finish( stdout, stderr, job_exit_code ) File "/mnt/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 962, in finish if ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and self.app.config.retry_metadata_internally ): File "/mnt/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 638, in external_metadata_set_successfully rval, rstring = simplejson.load( open( metadata_files.filename_results_code ) ) File "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py", line 328, in load use_decimal=use_decimal, **kw) File "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py", line 384, in loads return _default_decoder.decode(s) File "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py", line 402, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/mnt/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py", line 420, in raw_decode raise JSONDecodeError("No JSON object could be decoded", s, idx) JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) Tool execution generated the following error message: Unable to finish job </quote> Reading the code, this is breaking after all the child jobs have finished, and the data has been merged, during the external set metadata step. This specific example was BLAST XML output, and the merge had produced a 4.2 GB file which ended mid record (evidently the output merge was not really successful). However, as a partial XML file, it would be invalid and might this cause problems with something in the metadata setting code - and explain the reported error? Peter

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error in workflow
by Milad Bastami 12 Mar '14

12 Mar '14

Dear Galaxy Developers,I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size).I will appreciate your helpTraceback (most recent call last): File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish self.sa_session.flush() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/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 "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/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 "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush transaction.commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit t[1].commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit self._do_commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit self.connection._commit_impl() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl self.engine.dialect.do_commit(self.connection) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit connection.commit() OperationalError: (OperationalError) database is locked None None

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