- galaxy-dev - lists.galaxyproject.org

(no subject)
by Игорь Заигрин 05 Dec '12

05 Dec '12

Hi, Is it possible to display different content of central area (welcome.html) according to user - registered or guest? If guest - page with offer to register, if registered user - page with another info. And how I can get the email of this user? Thanks for your help! Igor.

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Key error in latest build of galaxy-central
by Anthonius deBoer 05 Dec '12

05 Dec '12

Got this when trying to install GMAP from the tool shed... Any ideas? Error Traceback: View as: Interactive | Text | XML (full) ⇝ KeyError: 'includes_repository_dependencies' URL: http://srv151/admin_toolshed/prepare_for_install?tool_shed_url=http://tools… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1070 in prepare_for_install view >> includes_repository_dependencies = util.string_as_bool( repo_information_dict[ 'includes_repository_dependencies' ] ) KeyError: 'includes_repository_dependencies'

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Running galaxy on multiple, physical servers
by Anthonius deBoer 04 Dec '12

04 Dec '12

Hi, I am trying to figure out how to run galaxy distributed over several physical servers, with different IP addresses... The wiki on scaling and load balancing only speaks of balancing on the same physical server, but does not address how to put a handful of managers on a different physical server... Any ideas how to do this? I guess I can just copy the .ini file, define managers in that and try to start it on that server, but I am hesitant until I know this can work at all... Thanks http://wiki.galaxyproject.org/Admin/Config/Performance/Web%20Application%20… Thon

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Can't find new pause / resume functionality in Dec 2012 Galaxy
by Greg Edwards 04 Dec '12

04 Dec '12

Hi all, I was keen to try the new Pause / Resume functionality mentuioned in http://wiki.galaxyproject.org/News/2012_12_03_DistributionNewsBrief but can't see it anywhere, in Galaxy or searches. It's not on the Test site at https://test.g2.bx.psu.edu/ or production at https://main.g2.bx.psu.edu/ Can you point me to where I can try it ? Thanks, -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

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Required Galaxy umask settings for HTML downloads?
by Josh Nielsen 04 Dec '12

04 Dec '12

Hello all, I am having issues downloading HTML files from Galaxy the same as is described in this email chain: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-August/010965.html I am getting the error "(13)Permission denied: xsendfile: cannot open file: /basedir/galaxy_data/database/tmp/tmp8iEccn/library_download.zip" which is indeed a basic filesystem permissions issue. The problem is that the permissions created for that directory and every directory created in tmp/ look like this: drwx------+ 2 galaxy galaxy 3 Dec 4 09:23 tmp8iEccn And I have placed the Apache user in the galaxy group, but as you can see no group permissions ever get set by Galaxy on the directories that it creates (it is getting a 700 permissions setting). As Nate Coraor suggested in the message linked to above, I have tried altering the default umask but I ran into issues with getting non-existant results. I use "sudo service galaxy start" as the galaxy user each time to start the server and a "ps -ef | grep galaxy" confirms that Galaxy is running as the galaxy user. Since I use sudo though I changed the sudoers file to include: root ALL=(ALL) ALL galaxy ALL=(ALL) ALL Defaults umask_override Defaults umask = 0002 This changed absolutely nothing. Then I started looking deeper into the PAM configuration and added a umask directive to /etc/pam.d/sudo (and also tried it in password-auth-ac and system-auth-ac) like this: "session optional pam_umask.so umask=0002". Still nothing changed in the permissions in tmp/ when I tried to download an HTML file: no group permissions were set. Then I dug deeper still and saw that sometimes if setting the mask in /etc/pam.d/ config files is not enough that you can try to set a system-wide mask in /etc/login.defs (following the suggestion here: http://stackoverflow.com/questions/10220531/how-to-set-system-wide-umask) Still no dice. I've pretty much exhausted my know-how in this department. Any other suggestions of how to fix this or where the correct place to set the umask is? Thanks, Josh Nielsen

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Re: [galaxy-dev] Speed up the galaxy
by Ido Tamir 04 Dec '12

04 Dec '12

> Hi all, > > How can I speed up the galaxy? Like how to use more cores and memeries. http://wiki.galaxyproject.org/Admin/Config/Performance/Production%20Server http://wiki.galaxyproject.org/Admin/Config/Performance/Web%20Application%20… HTH, ido

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Same error, better formatting.
by Franco Caramia 04 Dec '12

04 Dec '12

URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+… Module paste.exceptions.errormiddleware:*143* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> app_iter *=* self*.*application*(*environ*,* start_response*)* Module paste.debug.prints:*98* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> environ*,* self*.*app*)* Module paste.wsgilib:*539* in intercept_output >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*184* in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.web.controllers.admin_toolshed:*350* in browse_repositories >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*reselect_tool_panel_section*(* trans*,* ****kwd *)* Module galaxy.web.framework:*184* in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.web.controllers.admin_toolshed:*1352* in reselect_tool_panel_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> status*=*status *)* Module galaxy.web.framework:*746* in fill_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework:*757* in fill_template_mako >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* template*.*render*(* ****data *)* Module mako.template:*296* in render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> ****_kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> callable_*(*context*,* ***args*,* ****kwargs*)* Module _base_mako:*42* in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:*76* in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> __M_writer*(*unicode*(*render_tool_dependency_section*(* install_tool_dependencies_check_box*,* *[* repo_info_dict *]* *)**)**)* Module _admin_tool_shed_repository_common_mako:*204* in render_render_tool_dependency_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> changeset_revision *)* Module posixpath:*67* in join >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa…> *elif* path *==* '' *or* path*.*endswith*(*'/'*)**:* *AttributeError: 'NoneType' object has no attribute 'endswith'*

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Main toolshed broken??
by Franco Caramia 04 Dec '12

04 Dec '12

Hi list, Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error.. This is the repo: http://fcaramia@toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_b ismark Is anyone having the same issues?? I could just delete the repository but no option for that is given.. Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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workflow input param issue
by Marc Logghe 04 Dec '12

04 Dec '12

Hi, I have a workflow that basically needs a select parameter as input. 2 steps in the workflow actually need the very same input. I don't think there is a (easy) way to let the user only input the parameter once and that it is passed to both steps. Anyhow, currently - as a workaround and not very user friendly - the user needs to input the very same parameter twice, for each step where that parameter is required. The first issue however, is that as soon as the first parameter is set, the second is set as well apparently (they have the same name, that could explain) which is fine, but not to the chosen one, eg. both are kind of reset to default. No errors or something, simply reset, which makes it impossible to enter the parameter. Next, I hoped to solve the issue by upgrading galaxy to the most recent version. This was not the case since the workflow did not run at all anymore, which brings me to the second issue (see exception dump below). Any ideas anyone ? Thanks and regards, Marc Error - <type 'exceptions.AttributeError'>: 'list' object has no attribute 'output_name' URL: http://smith:8889/workflow/run?id=4b187121143038ff File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1523 in run enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 836 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 847 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 171 in render_body __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 40 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 435 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 338 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 498 in render_row_for_param __M_writer(unicode(conn.output_name)) AttributeError: 'list' object has no attribute 'output_name' ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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Re: [galaxy-dev] pass more information on a dataset merge
by Alex.Khassapov＠csiro.au 04 Dec '12

04 Dec '12

Hi John, My colleague (Neil) has a bit of a problem with the multi file support: When I try and use the option "Upload Directory of files" I get the error below Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'Bunch' object has no attribute 'multifiles' URL: http://140.253.78.218/library_common/upload_library_dataset Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.library_common:855 in upload_library_dataset view >> **kwd ) Module galaxy.web.controllers.library_common:1055 in upload_dataset view >> json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) Module galaxy.tools.actions.upload_common:342 in create_paramfile view >> multifiles = uploaded_dataset.multifiles, AttributeError: 'Bunch' object has no attribute 'multifiles' Any ideas? Should we check if 'multifiles' attribute is set? Or some other call is missing which should set it to NULL if it's missing? -Alex -----Original Message----- From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton Sent: Wednesday, 17 October 2012 3:21 AM To: Khassapov, Alex (CSIRO IM&T, Clayton) Subject: Re: [galaxy-dev] pass more information on a dataset merge Wow, thanks for the rapid feedback! I have made the changes you have suggested. It seems you must be interested in this idea/implementation. Let me know if you have specific use cases/requirements in mind and/or if you would be interested in write access to the repository. -John On Mon, Oct 15, 2012 at 11:51 PM, <Alex.Khassapov(a)csiro.au> wrote: > Hi John, > > I tried your galaxy-central-homogeneous-composite-datatypes implementation, works great thank you (and Jorrit). > > A couple of fixes: > > 1. Add multi_upload.xml to too_conf.xml 2. > lib/galaxy/tools/parameters/grouping.py line 322 (in get_filenames( context )) - > "if ftp_files is not None:" > Remove "is not None" as ftp_files is empty [], but not None, then line 331 "user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email )" throws an exeption if ftp_upload_dir isn't set. > > Alex > > -----Original Message----- > From: galaxy-dev-bounces(a)lists.bx.psu.edu > [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of John Chilton > Sent: Tuesday, 16 October 2012 1:07 AM > To: Jorrit Boekel > Cc: galaxy-dev(a)lists.bx.psu.edu > Subject: Re: [galaxy-dev] pass more information on a dataset merge > > Here is an implementation of the implicit multi-file composite datatypes piece of that idea. I think the implicit parallelism may be harder. > > https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-dat > atypes/compare > > Jorrit do you have any objection to me trying to get this included in galaxy-central (this is 95% code I stole from you)? I made the changes against a clean galaxy-central fork and included nothing proteomics specific in anticipation of trying to do that. I have talked with Jim Johnson about the idea and he believes it would be useful his mothur metagenomics tools, so the idea is valuable outside of proteomics. > > Galaxy team, would you be okay with including this and if so is there anything you would like to see either at a high level or at the level of the actual implementation. > > -John > > ------------------------------------------------ > John Chilton > Senior Software Developer > University of Minnesota Supercomputing Institute > Office: 612-625-0917 > Cell: 612-226-9223 > Bitbucket: https://bitbucket.org/jmchilton > Github: https://github.com/jmchilton > Web: http://jmchilton.net > > On Mon, Oct 8, 2012 at 9:24 AM, John Chilton <chilton(a)msi.umn.edu> wrote: >> Jim Johnson and I have been discussing that approach to handling >> fractionated proteomics samples as well (composite datatypes, not the >> specifics of the interface for parallelizing). >> >> My perspective has been that Galaxy should be augmented with better >> native mechanisms for grouping objects in histories, operating over >> those groups, building workflows that involve arbitrary numbers of >> inputs, etc... Composite data types are kindof a kludge, I think they >> are more useful for grouping HTML files together when you don't care >> about operating on the constituent parts you just want to view pages >> a as a report or something. With this proteomic data we are working >> with, the individual pieces are really interesting right? You want to >> operate on the individual pieces with the full array of tools (not >> just these special tools that have the logic for dealing with the >> composite datatypes), you want to visualize the files, etc... Putting >> these component pieces in the composite data type extra_files path >> really limits what you can do with the pieces in Galaxy. >> >> I have a vague idea of something that I think could bridge some of >> the gaps between the approaches (though I have no clue on the >> feasibility). Looking through your implementation on bitbucket it >> looks like you are defining your core datatypes (MS2, CruxSequest) as >> subclasses of this composite data type (CompositeMultifile). My >> recommendation would be to try to define plain datatypes for these >> core datatype (MS2, CruxSequest) and then have the separate composite >> datatype sort of delegate to the plain datatypes. >> >> You could then continue to explicitly declare subclasses of the >> composite datatype (maybe MS2Set, CruxSequestSet), but also maybe >> augement the tool xml so you can do implicit data type instances the >> way you can with tabular data for instance (instead of defining >> columns you would define the datatype to delegate to). >> >> The next step would be to make the parallelism implicit (i.e pull it >> out of the tool wrapper). Your tool wrappers wouldn't reference the >> composite datatypes, they would reference the simple datatypes, but >> you could add a little icon next to any input that let you replace a >> single input with a composite input for that type. It would be kind >> of like the run workflow page where you can replace an input with a >> multiple inputs. If a composite input (or inputs) are selected the >> tool would then produce composite outputs. >> >> For the steps that actually combine multiple inputs, I think in your >> case this is perculator maybe (a tool like interprophet or Scaffold >> that merges peptide probabilities across runs and groups proteins), >> then you could have the same sort of implicit replacement but instead >> of for single inputs it could do that for multi-inputs (assuming the >> Galaxy powers that be accept my fixes for multi-input tool parameters: >> https://bitbucket.org/galaxy/galaxy-central/pull-request/76/multi-input-dat…) >> >> The upshot of all of that would be that then even if these composites >> datatypes aren't used widely, other people could still use your >> proteomics tools (my users are definitely interested in Crux for >> instance) and you could then use other developers' proteomic tools >> with your composite datatypes even though they weren't designed with >> that use case in mind (I have msconvert, myrimatch, idpicker, >> proteinpilot, Ira Cooke has X! Tandem, OMSSA, TPP, and NBIC has an >> entire suite of label free quant tools). A third benefit would be >> that people working in other -omicses could make use of the >> homogenous composite datatype implementation without needing to >> rewrite their wrappers and datatypes. >> >> There is probably something that I am missing that makes this very >> difficult, let me know if you think this is a good idea and what its >> feasibility might be. I forked your repo and set off to try to >> implement some of this stuff last week and I ended up with my galaxy >> pull requests to improve batching workflows and multi-input tool >> parameters instead, but I hope to eventually get around to it. >> >> -John >> >> ------------------------------------------------ >> John Chilton >> Senior Software Developer >> University of Minnesota Supercomputing Institute >> Office: 612-625-0917 >> Cell: 612-226-9223 >> Bitbucket: https://bitbucket.org/jmchilton >> Github: https://github.com/jmchilton >> Web: http://jmchilton.net >> >> On Mon, Oct 1, 2012 at 8:24 AM, Jorrit Boekel >> <jorrit.boekel(a)scilifelab.se> wrote: >>> Dear list, >>> >>> I thought I was working with fairly large datasets, but they have >>> recently started to include ~2Gb files in sets of >50. I have ran >>> these sort of things before as merged data by using tar to roll them >>> up in one set, but when dealing with >100Gb tarfiles, Galaxy on EC2 >>> seems to get very slow, although that's probably because of my >>> implementation of dataset type detection (untar and read through files). >>> >>> Since tarring/untarring isn't very clean, I want to switch from >>> tarring to creating composite files on merge by putting a tool's >>> results into the dataset.extra_files_path. This doesn't seem to be >>> supported yet, because we currently pass in do_merge the output >>> dataset.filename to the respective datatype's merge method. >>> >>> I would like to pass more data to the merge method (let's say the >>> whole dataset object) to be able to get the composite files directory and 'merge' >>> the files in there. Good idea, bad idea? If anyone has views on >>> this, I'd love to hear them. >>> >>> cheers, >>> jorrit >>> >>> ___________________________________________________________ >>> 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/

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