galaxy-dev July 2011

galaxy-dev@lists.galaxyproject.org

79 participants
166 discussions

importing annotation with dataset
by Davide Cittaro 01 Jul '11

01 Jul '11

Hi, is it just me or when I try to import a dataset from a library to a history, annotation is not retained (whereas "info" is)? d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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importing into history from library
by Glen Beane 01 Jul '11

01 Jul '11

We're running the latest galaxy-dist and noticed a problem importing files from libraries into our history. If we click the down arrow to the right of a dataset and choose "Import this dataset into selected histories" it works fine, however if our datasets are in folders within the library and we select multiple datasets and then do "Import selected datasets into histories" nothing happens. If I go to a library with datasets that are not in a folder then selecting multiple works. Has anyone else seen this? -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

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Using the tool after log in
by shashi shekhar 01 Jul '11

01 Jul '11

Hi All, I have local instance of galaxy . I want to make changes in such a way that after log in, user should able to submit any job or run any tool. Log in should be compulsory to run any tool including upload tool. Whenever someone clicks on tool without log in ,it should display message like "You must be logged in <http://192.168.62.51:8089/user/login?webapp=galaxy> to use Galaxy" . Reagrds shashi shekhar

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Galaxy forgetting history and giving me new blank history
by Leandro Hermida 01 Jul '11

01 Jul '11

Having a very strange problem in the Galaxy web GUI that suddenly just started happening yesterday, getting very strange behavior in the history right panel. - Most of the time when I click on something in the GUI like to go to a tool page or to go to the Admin interface and come back suddenly Galaxy just replaces my current history and gives me a brand new history, its like it forgets what history I'm working with - In tool forms sometimes input data drop downs don't have anything in them even though there are datasets in my history that are of the right datatype. Could be related to problem above where it thinks maybe I'm in a new blank history Anyone have this ever happen? regards, Leandro

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public datasets/histories with external auth
by Shantanu Pavgi 01 Jul '11

01 Jul '11

Hi, We have a galaxy server setup using external shibboleth authentication. While we would like to have site behind authentication realm, there are instances when our galaxy datasets/histories need to be accessible publicly from other websites. We tried adding an exception to auth rule for /datasets path using Location directive in apache web server configuration, however galaxy server returned an error as: {{{ Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. }}} Is there any way to share public histories and datasets when galaxy is using external authentication mechanism? I have thought about setting up (fake) anonymous REMOTE_USER variable for /datasets path, but not sure whether this is correct approach. Also, would it require any galaxy code changes? Any thoughts? Thanks, Shantanu.

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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets
by Kip Bodi 01 Jul '11

01 Jul '11

Hi all, I'm having the same problem. I have a script that tries to take several history data sets as a single input: <command interpreter="perl">aggregate.pl --out $outfile $list_of_items_in_history</command> <inputs> <param format="txt" name="fitness_tables" type="data" multiple="true" label="Fitness score table, per site"/> </inputs> <outputs> <data format="tabular" name="outfile" /> </outputs> If I select only one history item it works, but if I press 'ctrl' to select multiple items, it fails: File '/storage/apps/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/lib/python2.6/site-packages/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/lib/python2.6/site-packages/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/storage/apps/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/storage/apps/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 979 in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1271 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/actions/__init__.py', line 360 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1274 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 79 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 110 in value_to_basic return self.to_string( value, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 1457 in to_string return value.id AttributeError: 'list' object has no attribute 'id' Is using multiple history items as a single input not currently supported, or is there something else I'm doing wrong? Cheers, Kip On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida <softdev(a)leandrohermida.com>wrote: > Hi again, > > Sorry to ping again about this, just very interested in knowing if > this is a missing feature in Galaxy or if I had configured something > wrong. > > Is it possible in Galaxy to have a tool with a multiple="true" input > dataset parameter? It doesn't seem so? > > best, > Leandro > > > On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida > <softdev(a)leandrohermida.com> wrote: > > Hi Nate, > > > > Thanks for the ping, have fun at the conference! > > On Tue, May 24, 2011 at 11:22 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > >> > >> Hi Leandro, > >> > >> The Galaxy Team has recently been preparing for and traveling in advance > >> of the Galaxy Community Conference, which begins today. Unfortunately I > >> don't have an answer for you, but when we're all back at work next week, > >> someone should be able to respond. > >> > >> Thanks, > >> --nate > >> > >> Leandro Hermida wrote: > >> > Hi again, > >> > > >> > Very sorry to ask again, just gotten no repsonse, but is this a Galaxy > >> > bug > >> > or does anyone have a functioning tool that takes multiple datasets as > >> > an > >> > input parameter??? i.e. > >> > > >> > <param type="data" multiple="true" ... /> > >> > > >> > regards, > >> > Leandro > >> > > >> > On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida > >> > <softdev(a)leandrohermida.com > >> > > wrote: > >> > > >> > > Hi again, > >> > > > >> > > I tried changing the format to txt and tabular which I have other > >> > > datasets > >> > > in my history and still the same error and stack trace in Galaxy. > >> > > > >> > > Is it possible at all to have a select multiple of datasets as an > >> > > input > >> > > parameter?? > >> > > > >> > > best, > >> > > Leandro > >> > > > >> > > > >> > > On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida < > >> > > softdev(a)leandrohermida.com> wrote: > >> > > > >> > >> Hi Galaxy developers, > >> > >> > >> > >> Something seems maybe to be wrong with the format="html" type... I > >> > >> forgot > >> > >> to add before that my tool input param the format="html" attribute: > >> > >> > >> > >> <param type="data" multiple="true" format="html" name="input1" /> > >> > >> > >> > >> In another tool I have it outputs format="html" and this works and > >> > >> displays in Galaxy just fine. I would like to use multiple of these > >> > >> output > >> > >> datasets in my history as the input for this other tool but > something > >> > >> seems > >> > >> to be wrong if you try to do this? > >> > >> > >> > >> a bit lost, > >> > >> Leandro > >> > >> > >> > >> > >> > >> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida < > >> > >> softdev(a)leandrohermida.com> wrote: > >> > >> > >> > >>> Hi, > >> > >>> > >> > >>> I have a tool where the input is multi-select of datasets, e.g.: > >> > >>> > >> > >>> <param type="data" multiple="true" name="input1" /> > >> > >>> > >> > >>> I tested it to see what it would pass to my command and I get the > >> > >>> following debug page and error in Galaxy: > >> > >>> > >> > >>> AttributeError: 'list' object has no attribute 'missing_meta' > >> > >>> > >> > >>> The last part of the stack trace looks like: > >> > >>> > >> > >>> >> validator.validate( value, history ) > >> > >>> Module galaxy.tools.parameters.validation:185 in validate > >> > >>> > >> > >>> history <galaxy.model.History object at 0xb8ea190> > >> > >>> self <galaxy.tools.parameters.validation.MetadataValidator > >> > >>> object > >> > >>> at 0xb8e6250> > >> > >>> value [<galaxy.model.HistoryDatasetAssociation object at > 0xa255550>, > >> > >>> <galaxy.model.HistoryDataset ... Association object at 0xb8ea210>] > >> > >>> > >> > >>> >> if value and value.missing_meta( check = self.check, skip = > >> > >>> >> self.skip > >> > >>> ): > >> > >>> AttributeError: 'list' object has no attribute 'missing_meta' > >> > >>> > >> > >>> What am I doing wrong? > >> > >>> > >> > >>> regards, > >> > >>> Leandro > >> > >>> > >> > >>> > >> > >> > >> > > > >> > >> > ___________________________________________________________ > >> > 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/ > >> > > > > > > ___________________________________________________________ > 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/ > -- Kip Lord Bodi Jr. Tufts University School of Medicine 136 Harrison Avenue, South Cove 502 Boston, MA 02118 617-636-3763 kip.bodi(a)tufts.edu www.tucf.org | genomics.med.tufts.edu

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galaxy-dev July 2011