July 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Several errors from run.sh
by charlie 06 Jul '11

06 Jul '11

> Hi all, > > I am upgrading to the most recent galaxy-dist 720455407d1c<https://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c> > . > First time run.sh shows following errors as in attachment. > It seems when I use 'manage_db.sh upgrade' it doesn't create necessary > tables for these tools. > Wonder if these are known issues? > > Thanks > > >

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Re: [galaxy-dev] [galaxy-user] double login / deleting users
by Nate Coraor 06 Jul '11

06 Jul '11

Joseph Hargitai wrote: > > Hi, > > 1, > referencing old thread: > http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html > > is the delete functionality still status-quo? i.e - there is no delete other than the workaround? Hi Joe, Since this is regarding a local installation, I've moved this thread to the galaxy-dev list. I believe you still need the workaround, yes. > 2, > switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab - By any chance, are you using require_login = True in the config? Which logout link are you clicking to get to that page? Thanks, --nate > > joe > ___________________________________________________________ > 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/

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adding qseq2fastq tool to the main instance
by Mete Civelek 06 Jul '11

06 Jul '11

Hi, Is it possible to add the qseq2fastq tool developed by vipints (found under repositories) to the Galaxy web portal (the central server, not my own instance of Galaxy)? I believe this would be a popular tool used by many Illumina users? Best Regards, Mete Civelek ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Bam to fastq
by Zschunke, Aaron M. 06 Jul '11

06 Jul '11

Hi, Is there any way to convert a certain section of a bam file to fastq using the galaxy tools? I just want to convert a certain part of the genome. Thanks. Aaron

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Cleanup scripts - question or bug ?
by Assaf Gordon 06 Jul '11

06 Jul '11

Hi, I'm trying to use the built-in cleanup scripts (instead of my own), came across a possible bug: 1. When running "delete_datasets.sh", the "info_only" flag is ignored. This is evident by running it twice with "-i" and getting different results (the second time - no datasets are deleted). 2. When running "purge_datasets.sh" with the "info_only" flag, no information is printed at all, making it impossible to know what would be purged without the "-i" flag. The only way to see what is purged is actually purging the datasets (kind of defeats the purpose of "info only"). I think the attached patch fixes both issues. 3. The relevant wiki page (https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa…) says about "delete_datasets.sh": "The purge_datasets.sh script will need to be run afterwards to remove the base datasets from disk." But the example on the wiki page (and in the script) has "-r" - so the files are actually deleted from the disk by "delete_datasets.sh". Does one still need to run "purge_datasets.sh" if used "-r" with "delete_datasets.sh" ? 4. If I accidentally run "purge_datasets.sh" without "-r" = is there a way to delete the stale files ? if not, perhaps the script should require either "-i" or "-r" to avoid such cases (or provide another cleanup script?) comments are welcomed, -gordon

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New Tool Shed: Inconsistent field names
by Peter Cock 06 Jul '11

06 Jul '11

Hi all, I've noticed some inconsistencies in the new tool shed. First of all the table view uses "Name" and "Description" for fields shown as "Name" and "Synopsis" on the tool details page. Also the field "Name" is not showing the tool name or tool suite name - they are showing the tool or tool suite ID. I would suggest using three columns / text boxes: ID, Name, Description e.g. based on the current XML file for this tool of mine, ID: seq_filter_by_id Name: Filter sequences by ID Description: from a tabular file I have previously commented on the problem with showing the "description" on its own without the context of the tool name as displayed in Galaxy: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html and: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html One idea would be to show just the name in the left hand pane of Galaxy, with the description as a tool tip AND show this at the top of the tool main page in the central panel. This would encourage tool authors to write this field as a self contained synopsis, and make the left hand panel less text heavy. Peter

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missing link 'display at UCSC'
by colin molter 05 Jul '11

05 Jul '11

Hello all, sorry for the very basic question (I tried to find some answer on the mailing list or faq but without any success). So here is my problem: i installed a fresh copy of galaxy in my server with apache. everything looks fine (i managed to perform several analyses so far). The problem is that there is *no link to UCSC*!! For my BAM file, i just have: display at Ensembl Current<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl…> And for the pileup: view in GeneTrack<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/genetra…> display at Ensembl Current<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl…> any idea bout how to have this link back. thks again colin -- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/

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Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets
by Kip Bodi 05 Jul '11

05 Jul '11

Hi Leandro, Thanks! I had to change one line to get it working: <command interpreter="perl"> ... #for $i in $add_inputs ${i.extra_table.file_name} #end for </command> <repeat name="add_inputs" title="Extra Fitness Tables"> <param format="txt" name="extra_table" type="data" label="Another fitness table" /> </repeat> Now galaxy will provide a list of files as the last parameters to the script. Best, Kip On Fri, Jul 1, 2011 at 3:53 AM, Leandro Hermida <softdev(a)leandrohermida.com>wrote: > Hi Kip, > > For the time being we are using this method to achieve the same > result, although its not as nice as just having a multi-select menu in > the form: > > <command> > ... > $input1 > #for $r in $add_inputs > $r.$input2 > #end for > ... > </command> > > In <inputs>: > > <param name="input1" type="data"/> > <repeat name="add_inputs"> > <param name="input2" type="data" /> > </repeat> > > > best, > Leandro > > > On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi <kip.bodi(a)tufts.edu> wrote: > > Sorry, I tried to edit that, to make it simpler, but missed the <param> > > block. The 'name' does match the one in the 'command' on my end > > (list_of_items_in_history). > > > > On Thu, Jun 30, 2011 at 10:45 AM, Kip Bodi <kip.bodi(a)tufts.edu> wrote: > >> > >> 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 > > > > > > > > -- > > 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 > > > -- 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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New tool shed: "Detailed description" fields are all empty
by Peter Cock 05 Jul '11

05 Jul '11

Hi all, I see there has been some work done on the new tool shed to support long descriptions again (a regression): https://bitbucket.org/galaxy/galaxy-central/changeset/372577e7bc6a However, the old data seems to have been lost - the "Detailed description" fields are all empty - any text entered on the old pre-hg ToolShed has been lost. Should I file a bug, or is it too late to rescue the old meta data? Thanks, Peter

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fasta integration in galaxy
by B M 05 Jul '11

05 Jul '11

Dear All, I have just finished integrating my blast data to my galaxy local instance, and now I would like to add my fasta files. Does anybody know how can I do that ? How should it look in the UI ? Thanks, best regards Ben

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