- galaxy-dev - lists.galaxyproject.org

Viewing Galaxy in Ipad
by Ganote, Carrie L 09 Jan '13

09 Jan '13

Hi all, There is a problem when viewing Galaxy from the Ipad if the Tool or History menu needs to scroll. Iframes do not render scrolling properly on Ios5 or later (even when using 2-finger scroll method). Has anyone had this issue and been able to fix it? We're showing off Galaxy at the PAG conference and we'll be using Ipads to display the page. Right now I'm trying to wrap contents of the toolMenuContainer in a div with style="-webkit-overflow-scrolling: touch;", but I could use some help since the toolMenu containing the tools gets inserted before my div. If I could just have it render one line down: Source looks like: <body class="toolMenuContainer"> <div class="toolMenu"> ..Tools.. </div> <div class="menuWrapper"> <div class="toolMenu"> ..Workflow.. </div> </div> </body> Thanks, Carrie Ganote

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Re: [galaxy-dev] backtrace when attempting to view a shared workflow
by Langhorst, Brad 08 Jan '13

08 Jan '13

I've recently updated to the december 20th revision of galaxy and still have a problem with a few workflows. You can find the backtraces below. based on these I'm starting to look in /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py - but any hints would be appreciated. thanks Brad here's a backtrace from an attempt to edit the problem workflow Error - <type 'exceptions.TypeError'>: 'NoneType' object is unsubscriptable URL: http://galaxy.neb.com/workflow/load_workflow?id=4280bfc7d7999071&_=13575670… File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 676 in load_workflow module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2130 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__'] TypeError: 'NoneType' object is unsubscriptable here's one attempting to run it File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1473 in run step.module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2130 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__'] TypeError: 'NoneType' object is unsubscriptable and here's the original report from an attempt to view a shared a workflow On Jan 2, 2013, at 9:59 PM, Brad Langhorst <langhorst(a)neb.com<mailto:langhorst@neb.com>> wrote: File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 202 in display_by_username_and_slug return self.display(trans, stored_workflow) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 218 in display self.get_stored_workflow_steps( trans, stored_workflow ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line 668 in get_stored_workflow_steps module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2120 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__'] TypeError: 'NoneType' object is unsubscriptable -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Installing dependencies from toolshed fails and produces strange folder
by Joachim Jacob 08 Jan '13

08 Jan '13

Hi all, Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies. So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike). After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here? Cheers and thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

2 1

variables not defined
by MONJEAUD 08 Jan '13

08 Jan '13

Hello all, I am using my own Galaxy instance and I had a problem with page and visualization tabs. For example, when I want to edit attributes of a page, I've got this error traceback : > |NameError: global name 'VALID_SLUG_RE' is not defined| and when I want to remove or share a page or a visualization, I've got this one : > |NameError: global name 'util' is not defined| To fix these errors, I added in the lib/galaxy/webapps/galaxy/controllers/page.py and lib/galaxy/webapps/galaxy/controllers/visualization.py these lines : > from galaxy import util > import re > VALID_SLUG_RE = re.compile( "^[a-z0-9\-]+$" ) So, I want to know if you know these problems or if it's only for my instance of galaxy. Maybe some files (where these variables are defined) are not present in my own galaxy. Cheers, Cyril Monjeaud -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17

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Get workflow info API problem
by Hagai Cohen 08 Jan '13

08 Jan '13

Hi, I'm trying to use the API for showing workflow info which should be something like: <url>/api/workflow/<workflow id> But I'm getting the following error: .../galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 80, in show label_name = step.tool_inputs['name'] TypeError: 'NoneType' object has no attribute '__getitem__' Which came from the following commit, two years ago: for step in latest_workflow.steps: if step.type == 'data_input': - inputs[step.id] = {'label':"Input Dataset", 'value':""} + inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. # p = step.get_required_parameters() What is step.tool_inputs and why is it None on my instance? (For my local installation, I changed to the following check: if step.type == 'data_input' and step.tool_inputs is not None - so the else will be triggered) Thanks, Hagai

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Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements 08 Jan '13

08 Jan '13

Hello all, Nominations are now open <http://bit.ly/gcc2013nom> for Training Day topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Any topic of interest to the Galaxy Community can be nominated<http://bit.ly/gcc2013nom>(see what was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January. Topic nomination closes 11 January. Thanks, Dave Clements, on behalf of the GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee> Links: http://bit.ly/gcc2013nom - nominate a topic http://bit.ly/gcc2013td - Training Day page http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Question about content of Galaxy installation package
by Uho Uho 07 Jan '13

07 Jan '13

Hi, I installed Galaxy locally. I would like to check with you if its installation package has everything necessary. galaxy-galaxy-dist-36ad8aa7b922.zip (checked today: 01/07/13) My main problem is that "NGS:Mapping section" does not look similar to the main Galaxy page. The downloaded package contains "Bowtie2" there but things like "Lastz", "BWA", "Bowtie" (bowtie1) are absent. I.e. there are no any XML files related to these software inside of "tools" folder (only bowtie2 related). Configuration files ("tool_*") inside of the main folder contain only references to "bowtie2". While my friends say that their version of files have references to the first bowtie. Can you please confirm that it's supposed to be like that and you removed things related to BWA/Bowtie/Lastz? And if yes, can you please indicate where I could find an older version of Galaxy distributive with them? If I'm doing something wrong, can you please tell me? Thank you, Uho.

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Uploading large files to history through API (some random thoughts)
by John Chilton 07 Jan '13

07 Jan '13

I went down something of a rabbit hole last night, I thought that uploading files through the API using multipart/form-data worked. It is only at the very end of my adventure that I realized it only works for libraries uploads. I think it would be great to get that working to histories as well. I cannot spend much more time on this right now (I thought I only needed to spend an hour to implement the client side stuff), but I thought I would post the progress I made here in case someone wants to take up the fight someday: The first thing is that when issuing multipart/form-data requests, inputs are not currently being deserialized from JSON (so for instance in the tools api code the "inputs" variable would be the string containing the json, not the python dictionary). To bring multipart/form-data requests in line with other content requests I modified this in ilb/galaxy/web/framework/__init__.py payload = kwargs.copy() named_args, _, _, _ = inspect.getargspec(func) for arg in named_args: payload.pop(arg, None) with this: payload = kwargs.copy() named_args, _, _, _ = inspect.getargspec(func) for arg in named_args: payload.pop(arg, None) for k, v in payload.iteritems(): if isinstance(v, (str, unicode)): try: payload[k] = simplejson.loads(v) except: # may not actually be json, just continue pass payload = util.recursively_stringify_dictionary_keys( payload ) One could also imagine doing this replacement in the tools api controller directly on payload['input'] instead. After that change, files still weren't being matched up with inputs properly: This debug statement I added to upload_common.py, demonstrates that file_data is None. galaxy.tools.actions.upload_common INFO 2012-11-27 00:22:17,585 Uploaded datasets is {'NAME': u'galxtest694734465387762969.txt', 'file_data': None, 'space_to_tab': None, 'url_paste': None, '__index__': 0, 'ftp_files': None} To address this, the files_*|file_data parameters need to be moved inside of the inputs dict. That means in lib/galaxy/webapps/galaxy/api/tools.py, changing this: inputs = payload[ 'inputs' ] To this: inputs = payload[ 'inputs' ] for k, v in payload.iteritems(): if k.startswith("files_"): inputs[k] = v Then the debug line becomes this: galaxy.tools.actions.upload_common INFO 2012-11-27 00:33:15,168 Uploaded datasets is {'NAME': u'galxtest2484272839208214846.txt', 'file_data': FieldStorage('files_0|file_data', u'galxtest2484272839208214846.txt'), 'space_to_tab': None, 'url_paste': None, '__index__': 0, 'ftp_files': None} Which matches pretty well with the same line coming from a web browser request: galaxy.tools.actions.upload_common INFO 2012-11-27 00:23:57,590 Uploaded datasets is {'NAME': u'', 'file_data': FieldStorage('files_0|file_data', u'second_step.png'), 'space_to_tab': None, 'url_paste': u'', '__index__': 0, 'ftp_files': None} These changes aside I still wasn't it sill didn't work, that is why this is a rambling e-mail and not a pull request. I got this exception http://pastebin.com/hhs1pjtP. I guess something to do with the session handling stuff being different between API calls and normal web calls. Anyway, I've inspected the actual requests I was generating and I think they are reasonable, Galaxy just needs to be augmented to accept them :). If someone does land up taking a look at this, I have committed my test case to blend4j so it can be used to really quickly test such a client request (requires git, Java, and maven): % git checkout git@github.com:jmchilton/blend4j.git % cd blend4j % mvn test -Dtest=ToolsTest -Dtest.galaxy.instance=http://localhost:8080/ -Dtest.galaxy.key=<testapikey> Thanks, -John

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Re: [galaxy-dev] History will not refresh after workflow submission via the API
by Carl Eberhard 07 Jan '13

07 Jan '13

Great. I'm glad it's working and thanks for your patience, Sascha. On Mon, Jan 7, 2013 at 5:35 AM, MSc. Sascha Kastens < s.kastens(a)gatc-biotech.com> wrote: > Hi Carl! > > > > My holidays were good, indeed. Hope you did have some time to relax, too. > > > > Thanks for your last update! Everything works as expected now! Thanks > thanks thanks! > > > > Have a nice week! > > > > Cheers, > > Sascha > > > > > > ------------------- > > > > Hello, Sascha > > > I’ve added some better handling for new datasets and now refresh the > history panel when a job completes with the force_history_refresh. > > > If you update to the latest revision, does your tool work as expected > now? > > > Hope your holidays were good, > > C > > > > On Fri, Dec 21, 2012 at 5:33 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Hey Carl! > > Thanks for this information and your work. I will be on holidays the next > two weeks. Therefore I cannot reply if you need more information or testing > from me. I wish you a Merry Christmas and a Happy New Year! > > Cheers, > > Sascha > > ----------- > > Hello Sascha, > > > I wanted to let you know this issue is still being worked on and that I > have some leads as to what’s going on. I may have a fix for this soon. I > appreciate your patience. > > > C > > > > On Mon, Dec 10, 2012 at 3:41 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > 1. How many datasets does your tool produce (in your test case)? > > - Two files > > 2. Does your tool produce datasets over time (that’s my assumption from > the errors we’ve had)? > > - My tool submits selected workflows and the datasets from the tools in > these worflow are added to > > the same history as where the submit-tool datasets are > > 3. If I understand, your first dataset appears, shows running, and (now) > goes green? > > - Yes, exactly > > 4. You’re other datasets never appear? > > - No, they appear. But I have to refresh the history manually >> > force_history_refresh="True" does not work > > anymore. > > S > > > > On Thu, Dec 6, 2012 at 4:35 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Hi Carl! > > It looks like you are getting closer. Now the output of the tool gets > green as soon as the job has finished but > > the history did not refresh automatically (force_history_refresh is set to > True). > > If you need any further information let me know! > > Thanks, > > Sascha > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: [galaxy-dev] History will not refresh after workflow submission via > the API > > Sent: > > Mittwoch, 5. Dezember 2012 19:03 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Hello again, Sascha > > > I’ve committed a change to galaxy-central that more gracefully handles > sync’ing histories and the HDAs they contain. > > > Can you update to the latest galaxy-central revision and try your tool > again? > > Thanks, > > C > > > > > On Fri, Nov 30, 2012 at 1:47 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Don’t worry, Carl! > > Thanks for you assistance and your quick response. > > Cheers, > > Sascha > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: [galaxy-dev] History will not refresh after workflow submission via > the API > > Sent: > > Donnerstag, 29. November 2012 20:38 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Sorry for the delay, Sascha. > > I think I’ve figured out what’s going on here. I’ll work on a fix which > should be available in central soon. > > > Thanks for your patience. > > C > > > > On Wed, Nov 28, 2012 at 2:22 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > This line is output right before the Job is running on the Cluster: > > The following ids have changed state: ["e721f81135f1bdf1", > "79b6b0e08a33fb04"] > > Then come some "normal" information lines, and finally: > > The following ids have changed state: > > [ > > "84f49fe0eab77e89" > > , > > "c7ed15b882f70e0c" > > , > > "a2fd9a049c3c1244" > > , > > "f2f5d3b2414fcb33" > > , > > "6a7868e6e99a9a29" > > , > > "7eefa465e388c990" > > , > > "f37a392459dba1d7" > > , > > "6a73de8a9c82cb0e" > > ] > > historyItem is undefined (line 277)... > > Cheers, Sascha > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: Re: Re: [galaxy-dev] History will not refresh after workflow > submission via the API > > Sent: > > Dienstag, 27. November 2012 17:01 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > That’s a good lead. Thanks. > > > It looks like some of the dataset ids in the history aren’t mapping > correctly. That line is looking up a particular dataset in the history by > it’s id. Galaxy uses two styles of ids: raw (e.g. ’12’) and encoded (e.g. > ’65hf39ef19’). The problem may be there. > > > Is this a local installation of Galaxy? In other words, can you alter > the code being used? > > If so, can you add the following to line 170 in > static/scripts/mvc/history/history-model.js: > > console.warn( ’The following ids have changed state:’, changedIds ); > > and try your workflow again (hopefully this isn’t too time-consuming)? > > > I’ll add some better error handling in that section. > > > > > On Tue, Nov 27, 2012 at 10:33 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Here it comes: > > historyItem is undefined (line 277) > > [image: [image]] > > historyItem.fetch(); > > > http://192.168.30.78:5454/static/scripts/mvc/dataset/hda-model.js?v=1354028… > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: Re: [galaxy-dev] History will not refresh after workflow submission > via the API > > Sent: > > Dienstag, 27. November 2012 15:08 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Good. As a start, that should allow you to see any errors in Galaxy’s > javascript (a client-side programming language) that might occur. > > > If you start firebug (by hitting F12) and run your workflow, do you see > any errors? > > > > > On Tue, Nov 27, 2012 at 2:17 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Firebug is installed! > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: [galaxy-dev] History will not refresh after workflow submission via > the API > > Sent: > > Montag, 26. November 2012 16:33 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Great! Do you have Firebug installed? > > > If not, could you install it, please? It will allow us to find > javascript errors more easily. > > https://getfirebug.com/ > > > > > > On Mon, Nov 26, 2012 at 10:22 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Hello Carl! > > Thanks for your personal assistance :-) > > I am using Firefox 13.0.1 > > Cheers, > > Sascha > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.eu> > > Subject: > > Re: Re: [galaxy-dev] History will not refresh after workflow submission > via the API > > Sent: > > Montag, 26. November 2012 16:15 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Hello, Sascha > > > So let’s see what the problem might be. > > > Which browser are you currently using? > > > > On Thu, Nov 22, 2012 at 4:01 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Hi Carl, > > I have updated to the latest revison but the error still occurs. > > Cheers, > > Sascha > > Original Message > > processed by CONSOLIDATE <http://www.consolidate.at> > > Subject: > > Re: [galaxy-dev] History will not refresh after workflow submission via > the API > > Sent: > > Mittwoch, 21. November 2012 17:54 > > From: > > Carl Eberhard (carlfeberhard(a)gmail.com) > > Hi Sascha, > > > This may be due to the recent history panel changes. Can you update to > the latest revision and see if the error still occurs? > > > Thanks, > > Carl > > > > On Tue, Nov 20, 2012 at 2:22 AM, MSc. Sascha Kastens < > s.kastens(a)gatc-biotech.com> wrote: > > Hi devs! > > After updating my local instance to changeset > 19cbbaf566216cb46ecc6a6d17e0f1e0ab52978e my tool which submits a workflow > via the > > API and set force_history_refresh to TRUE does not refresh the history > anymore. > > The job is submit via DRMAA to SGE. Unfortunately the job seems to run > forever because it is still in yellow state (even after SGE tells Galaxy > that the job has finished. As soon as I refresh the history manually the > according history entries get green and all entries for the submitted > workflow are shown. > > I have no idea where I can have a look at. If you need any further > information let me know! > > Thanks for your help in advance! > > Cheers, > > Sascha > > > ___________________________________________________________ > 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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How to get output images to appear in Galaxy
by Jennifer Hillman-Jackson 07 Jan '13

07 Jan '13

Repost to Galaxy Dev On 1/7/13 5:14 AM, Makis Ladoukakis wrote: > Dear Galaxy users, > > I have a tool which among other files it produces certain images in .png > format. Does anyone know if there is a way to make them appear inside > the "display data" interface? > > Thank you in advance, > Efthymios Ladoukakis > > > ___________________________________________________________ > 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/ > -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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