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

Re: [galaxy-dev] Issues with local instance of toolshed?
by Paul-Michael Agapow 17 Apr '12

17 Apr '12

Hi Amanda, > I've recently been trying to implement a local instance of the tool > shed, and have followed the tutorials on the wiki, but when I run sh > run_community.sh, it doesn't do anything. I have mercurial installed, > so that shouldn't be a problem, and I've used the example > community_wsgi.ini and run_community.sh. I can pastebin what I have if > it would help. Thank you in advance. Greg will probably have this fixed by the time I reply, but I had a similar problem, which resulted from me minsunderstanding or missing what had to be configured in the toolshed ini file. From my notes, set these vars, in a similar manner to the main Galaxy: - port & host: should be set to where you want the toolshed to be available from - database_file: use this is if you want to use the sqlite3 db. I had some problems with this, which were eventually solved by setting the path correctly for insertion in an sqlite protocol string (e.g. /database/community.sqlite for a relative path that puts the file in the database folder) - file_path: again, had some problems with this, which were solved by creating the directory for the file (e.g. <galaxy inst>/database/community_files) explicitly - admin_users: like the main Galaxy installation, for setting the admins ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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Re: [galaxy-dev] [galaxy-user] Toolshed initial upload errors out
by Greg Von Kuster 17 Apr '12

17 Apr '12

Hi paul, I've forwarded this thread to the galaxy-dev mail list as that is where these types of issues are discussed. Please keep the list included in your responses so that other interested parties can follow the thread. Regarding this issue, your initial problem was regarding uploading a file to a repository that you successfully created, but your pater log does not include anything about uploading. Can you clarify what the problem is? I'll need as much context as you can provide. For example, have you successfully created a new repository? If so, is the problem still that you cannot upload a file to it? If this is the case, can you send me the file you are attempting to upload? What are the contents of your hgweb.config file, which is located in you Galaxy install directory? Thanks, Greg Von Kuster On Apr 17, 2012, at 4:34 AM, Paul-Michael Agapow wrote: > Thanks Greg, > > Here’s the last bit, the last two failed attempts. Looks like it’s failing to find a temporary directory. Shouldn’t make any difference, but I’m running this out of a user account as I play round with the toolshed features. > > Cheers > > p > > transaction abort! > rollback completed > transaction abort! > rollback completed > 158.119.175.46 - - [10/Apr/2012:13:57:08 +0100] "POST /upload/upload?repository_id=adb5f5c93f827949 HTTP/1.1" 500 - "http://158.119.147.40:9009/ > upload/upload?repository_id=adb5f5c93f827949&webapp=community" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrom > e/17.0.963.78 Safari/535.11" > Error - <type 'exceptions.TypeError'>: array item must be char > 158.119.175.46 - - [10/Apr/2012:14:00:04 +0100] "GET /repository/browse_repositories?webapp=community&operation=my_repositories HTTP/1.1" 200 - > "http://158.119.147.40:9009/repository?webapp=community" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrome/17.0 > .963.78 Safari/535.11" > 158.119.175.46 - - [10/Apr/2012:14:00:06 +0100] "GET /repository/browse_repositories?f-deleted=False&f-email=pma(a)agapow.net&sort=name&show_item_ > checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949& HTTP/1.1" 302 - "http://158.119.14 > 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH > TML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > Exception OSError: (2, 'No such file or directory', '/tmp/tmpxiB8nn') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', > mode 'w+b' at 0xbc4d2a0>> ignored > 158.119.175.46 - - [10/Apr/2012:14:00:06 +0100] "GET /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele > ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1 HTTP/1.1" 200 - "http://158.119.147 > .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT > ML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > 158.119.175.46 - - [10/Apr/2012:14:00:11 +0100] "GET /upload/upload?repository_id=adb5f5c93f827949&webapp=community HTTP/1.1" 200 - "http://158. > 119.147.40:9009/repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-deleted=False&show_item_checkboxes=false&a > sync=false&webapp=community&operation=view_or_manage_repository&page=1" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gec > ko) Chrome/17.0.963.78 Safari/535.11" > transaction abort! > rollback completed > transaction abort! > rollback completed > 158.119.175.46 - - [10/Apr/2012:14:00:30 +0100] "POST /upload/upload?repository_id=adb5f5c93f827949 HTTP/1.1" 500 - "http://158.119.147.40:9009/ > upload/upload?repository_id=adb5f5c93f827949&webapp=community" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrom > e/17.0.963.78 Safari/535.11" > Error - <type 'exceptions.TypeError'>: array item must be char > 158.119.175.46 - - [10/Apr/2012:14:00:40 +0100] "GET /repository/browse_repositories?webapp=community&operation=my_repositories HTTP/1.1" 200 - > "http://158.119.147.40:9009/repository?webapp=community" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrome/17.0 > .963.78 Safari/535.11" > 158.119.175.46 - - [10/Apr/2012:14:00:44 +0100] "GET /repository/browse_repositories?f-deleted=False&f-email=pma(a)agapow.net&sort=name&show_item_ > checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949& HTTP/1.1" 302 - "http://158.119.14 > 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH > TML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > 158.119.175.46 - - [10/Apr/2012:14:00:44 +0100] "GET /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele > ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1 HTTP/1.1" 200 - "http://158.119.147 > .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT > ML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > 158.119.175.46 - - [10/Apr/2012:14:01:08 +0100] "GET /repository/browse_repositories?f-deleted=False&f-email=pma(a)agapow.net&sort=name&show_item_ > checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949& HTTP/1.1" 302 - "http://158.119.14 > 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH > TML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > Exception OSError: (2, 'No such file or directory', '/tmp/tmpTsL0B1') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', > mode 'w+b' at 0xbc4d840>> ignored > 158.119.175.46 - - [10/Apr/2012:14:01:08 +0100] "GET /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele > ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1 HTTP/1.1" 200 - "http://158.119.147 > .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories" "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT > ML, like Gecko) Chrome/17.0.963.78 Safari/535.11" > Removing PID file community_webapp.pid > > > > > ---- > Paul Agapow (paul-michael.agapow(a)hpa.org.uk) > Bioinformatics, Health Protection Agency > > From: Greg Von Kuster [mailto:greg@bx.psu.edu] > Sent: 16 April 2012 14:23 > To: Paul-Michael Agapow > Cc: 'galaxy-user(a)lists.bx.psu.edu' > Subject: Re: [galaxy-user] Toolshed initial upload errors out > > Hi Paul, > > On Apr 10, 2012, at 9:15 AM, Paul-Michael Agapow wrote: > > > As per the title, I’m trying to setup a toolshed for our local use. After creating a repo, I try to upload the initial file only to get: > > TypeError: array item must be char > > Which seems to happen repeatedly, i.e. it’s not a passing error. > > > I'll need to see your paster log to be able to help on this one. You can view it using "tail -f community_webapp.log" (without the quotes) from your Galaxy install directory. Can you respond back with the content? > > > > > While I’m here, a perhaps obvious question: where or how does the main Galaxy instance get the list of toolsheds to display? The main and test sheds are hardcoded in, I guess, but how does it pick up the local – simply by virtue of the fact that it is local? > > > The list of tool sheds available to any local Galaxy instance is defined in the tool_sheds_conf.xml file in the Galaxy install directory. For your local shed, you'll simply need to an entry like this: > > <tool_shed name="Bx tool shed" url="http://gvk.bx.psu.edu:9009/"/> > > > > > p > > ---- > Paul Agapow (paul-michael.agapow(a)hpa.org.uk) > Bioinformatics, Health Protection Agency > > Thanks, > > Greg Von Kuster > > > > > > > ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > > > ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ************************************************************************** >

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Issues with local instance of toolshed?
by Amanda Zuzolo 16 Apr '12

16 Apr '12

Hello all, I've recently been trying to implement a local instance of the tool shed, and have followed the tutorials on the wiki, but when I run sh run_community.sh, it doesn't do anything. I have mercurial installed, so that shouldn't be a problem, and I've used the example community_wsgi.ini and run_community.sh. I can pastebin what I have if it would help. Thank you in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity

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This link may not be followed from within Galaxy.
by Eli Reuveni 16 Apr '12

16 Apr '12

Hi, I am getting the error "This link may not be followed from within Galaxy." When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Best

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where can I find galaxy code documentation?
by Eli Reuveni 16 Apr '12

16 Apr '12

Hi, I have a local galaxy instance in my institute and have few basic questions: 1) I need to enable galaxy to upload large files from the local galaxy server without the need to use the ftp or the file upload module, is there an easy way to do it or do I need to write a special code? 2) I need to customize galaxy Python code (i.e., under the ~/galaxy-dist/lib directory). Where can I find documentation of the galaxy Python classes (using wiki or other format) Thanks in advanced,

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GCC2012 Abstract Submission Deadline is April 16, one week from today.
by Dave Clements 16 Apr '12

16 Apr '12

Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is April 16, one week from today. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, and hope to see you in Chicago, Dave C On Mon, Feb 13, 2012 at 3:27 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are now > being accepted for oral presentations at the 2012 Galaxy Community > Conference (GCC2012) <http://wiki.g2.bx.psu.edu/Events/GCC2012>. > Submissions on any topics of interest to the Galaxy community are > encouraged. Areas of interest include, but are not limited to: > > - Best practices for local Galaxy installation and management > - Integrating tools and/or data sources into the Galaxy framework > - Deploying galaxy on different infrastructures > - Compelling or novel uses of Galaxy for biomedical analysis > > See the GCC2011 program <http://wiki.g2.bx.psu.edu/Events/GCC2011> for an > idea of the breadth of topics that can be covered. Oral presentations will > be approximately 15-20 minutes long, including time for question and > answer. There will also be an opportunity for lightning talks, which will > be solicited at the meeting. The submission deadline is April 16. See the GCC2012 > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for > more details and how to submit. > > GCC2012 <http://wiki.g2.bx.psu.edu/Events/GCC2012> will be held, July > 25-27 in Chicago, Illinois, United States. The main meeting will run for two > full days <http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>, and be > preceded by a full day of training workshops<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>. > If you are a bioinformatics tool developer, data provider, workflow > developer, power bioinformatics user, sequencing or bioinformatics core > staff, or a data and analysis archival specialist, then GCC2012 is relevant > to you. Registration will open in March. > GCC2012 is hosted by the University of Illinois at Chicago<http://uic.edu/>, > the University of Illinois at Urbana-Champaign <http://illinois.edu/>, > and the Computation Institute <http://www.ci.anl.gov/>. > > Links: > http://galaxyproject.org/GCC2012 > http://galaxyproject.org/wiki/Events/GCC2012/Abstracts > > Thanks, > > Dave Clements > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://galaxyproject.org/wiki/ > > -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Re: [galaxy-dev] Workflow import error
by Greg Von Kuster 16 Apr '12

16 Apr '12

Hi Rob, When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? Thanks, Greg Von Kuster On Apr 16, 2012, at 10:07 AM, Robert Chase wrote: > Hi Greg, > > After I modified the modules.py file that bug went away, but now I'm getting a new error: > > Module galaxy.web.base.controller:420 in get_stored_workflow_steps view > << module = module_factory.from_workflow_step( trans, step ) > #Check if tool was upgraded > step.upgrade_messages = module.check_and_update_state() > # Any connected input needs to have value DummyDataset (these > # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() > AttributeError: 'NoneType' object has no attribute 'check_and_update_state' > > -Rob > > On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc(a)channing.harvard.edu> wrote: > Thanks Greg, > > I'll try to merge the change into my version. > > -Rob > > > On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Robert, > > Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update. > > Greg Von Kuster > > On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: > >> Hello All, >> >> I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line >> >> tool_version = self.__get_tool_version( trans, tool_id ) >> >> but if you look at the function definition containing that line, you see >> >> def from_workflow_step( Class, trans, step ): >> which does not half a self in it. Then we get an error. >> >> https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.p… >> >> -Rob >> ___________________________________________________________ >> 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/ > > >

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Workflow import error
by Robert Chase 16 Apr '12

16 Apr '12

Hello All, I have just tried to import a workflow file and when I try to view the workflow, I'm getting an error, "global name 'self' is not defined". Error Traceback: View as: Interactive<http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> (full) <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> | Text <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> (full) <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> | XML <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> (full) <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> ⇝ NameError: global name 'self' is not defined clear this clear this URL: http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e Module weberror.evalexception.middleware:*364* in respond <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> *try**:* __traceback_supplement__ *=* errormiddleware*.*Supplement*,* self*,* environ app_iter *=* self*.*application*(*environ*,* detect_start_response*)* *try**:* return_iter *=* list*(*app_iter*)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.debug.prints:*98* in __call__ <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> *try**:* status*,* headers*,* body *=* wsgilib*.*intercept_output*(* environ*,* self*.*app*)* *if* status *is* None*:* # Some error occurred>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>environ*, * self*.*app*)* Module paste.wsgilib:*539* in intercept_output <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> environ*[*'paste.recursive.script_name'*]* *=* my_script_name *try**:* *return* self*.*application*(*environ*,* start_response*)* *except* ForwardRequestException*,* e*:* middleware *=* CheckForRecursionMiddleware*(*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>*return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> *[**]**)**.*append*(*HTTPException*)* *try**:* *return* self*.*application*(*environ*,* start_response*)* *except* HTTPException*,* exc*:* *return* exc*(*environ*,* start_response*)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>*return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> kwargs*.*pop*(* '_'*,* None *)* *try**:* body *=* method*(* trans*,* ****kwargs *)* *except* Exception*,* e*:* body *=* self*.*handle_controller_exception*(* e*,* trans*,* ****kwargs *)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.controllers.workflow:*207* in display_by_id <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> # Get workflow. stored_workflow = self.get_stored_workflow( trans, id ) return self.display(trans, stored_workflow) def display(self, trans, stored_workflow):>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>*return* self*.*display*(*trans*,* stored_workflow*)* Module galaxy.web.controllers.workflow:*217* in display <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> # Get data for workflow's steps. self*.*get_stored_workflow_steps*(* trans*,* stored_workflow *)* # Get annotations. stored_workflow*.*annotation *=* self*.*get_item_annotation_str* (* trans*.*sa_session*,* stored_workflow*.*user*,* stored_workflow *)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>self*.* get_stored_workflow_steps*(* trans*,* stored_workflow *)* Module galaxy.web.base.controller:*418* in get_stored_workflow_steps <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view<http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> *if* step*.*type *==* 'tool' *or* step*.*type *is* None*:* # Restore the tool state for the step module *=* module_factory*.*from_workflow_step*(* trans* ,* step *)* #Check if tool was upgraded step*.*upgrade_messages *=* module*.* check_and_update_state*(**)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>module *= * module_factory*.*from_workflow_step*(* trans*,* step *)* Module galaxy.workflow.modules:*369* in from_workflow_step <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> """ type = step.type return self.module_types[type].from_workflow_step( trans, step ) module_factory = WorkflowModuleFactory( dict( data_input=InputDataModule, tool=ToolModule ) )>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#>*return* self*.*module_types*[*type*]**.*from_workflow_step*(* trans*,* step *)* Module galaxy.workflow.modules:*202* in from_workflow_step <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> view <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> << <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> # in addition to tool id, enhance the selection process here # to retrieve the correct version of the tool. tool_version *=* self*.*__get_tool_version*(* trans*,* tool_id *)* *if* tool_version*:* tool_version_ids *=* tool_version*.*get_version_ids*(* trans*.*app *)*>> <http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#> tool_version *=* self*.*__get_tool_version*(* trans*,* tool_id *)* *NameError: global name 'self' is not defined* Thankyou in advance for any help that you can give. -Rob

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Workflow Tags
by Frank Sørensen 16 Apr '12

16 Apr '12

Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of tags in the tag list doubles, and thus rapidly grows towards infinity, and there's not much I can do about it - except to avoid cloning workflows, which is a drag. I get this behavior regardless if the workflow I clone from is tagged or not. Has anyone else seen this? Is there a way to remove all tags from a workflow? Shouldn't a given tag be present only once in the tag list pr. workflow? Now I have the same five tags appearing hundreds of times in each tag-list, and they are very hard - if not impossible to get rid of. Kind Regards Frank Sorensen -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363

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Just wanted to say...
by Louise-Amélie Schmitt 16 Apr '12

16 Apr '12

I love the improvements you recently made to the web interface layout in galaxy-central, it's really neat! Collapsing the margins and making everything smoother makes the interface really easier to read. Thanks for the hard work, as always, L-A

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