galaxy-dev December 2016

galaxy-dev@lists.galaxyproject.org

39 participants
37 discussions

New datatypes with code dependencies
by Cristel Thomas 14 Dec '16

14 Dec '16

Hello, We'd like to add some datatypes to Galaxy specific to flow cytometry (finally). One of the datatype is a binary format which requires rpy2/R to be read (no good python module available to do that). How do you guys deal with that? Thanks, Cris

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multiple datatypes input in 16.07
by Cristel Thomas 14 Dec '16

14 Dec '16

Hi Galaxy Devs, We have a few tools with multiple datatypes as input. They work fine in 16.01. In 16.07 though, the selection of files in the tools' drop-downs include every single file in the history, instead of just the files from the specified data types. Anyone else run into this? Any idea of what's going on? Thanks much, Cris

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Testing workflows
by Eric Rasche 14 Dec '16

14 Dec '16

Wondering if anyone has tooling to test a workflow as it exists in a specific galaxy instance? I'm looking to test some of my user's manually built workflows in our galaxy instance to make sure that we can detect issues when they arise (e.g. due to changes in the interfaces of our non-toolshed installed tools) Ideally something like: $ my_tool $galaxy_url $api_key $workflow_id <set of files and their input IDs in the workflow> > report.xunit.xml If not we'll build something soon. Cheers, Eric

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Addind new datatype - best practice
by Floreline TOUCHARD 11 Dec '16

11 Dec '16

Hi Galaxy community, I would like to add custom datatypes to my Galaxy server without editing any Galaxy files if possible. I've already created and renamed a second config/datatype.conf file. Both files are listed into galaxy.ini (variable datatypes_config_file). But what about the new datatype Class ? For example if it's a binary class, how can I add this class without editing the binary.py file or any other file (if it's possible) ? Thanks in advance, Floreline

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Broken logo 'src' in masthead for Galaxy 16.07 served from subdirectory
by Peter Briggs 08 Dec '16

08 Dec '16

Dear developers Since upgrading to release_16.07 I've noticed a broken link to the masthead icon (i.e. the Galaxy logo 'galaxyIcon_noText.png') in our local Galaxy installations, which are all served from subdirectories of the webserver, e.g. https://centaurus.itservices.manchester.ac.uk/galaxy/ The icon is visible when this URL is visited but appears to be broken when using parts of Galaxy served from their own subdirectories e.g. the login page (under https://centaurus.itservices.manchester.ac.uk/galaxy/user/login?...) or the admin interface (https://centaurus.itservices.manchester.ac.uk/galaxy/admin). At the top level the logo <img> "src" is points correctly to "/galaxy/static/images/galaxyIcon_noText.png"; in the subdirs (users,admin etc) it points to "../../../static/images/galaxyIcon_noText.png" (which cannot be loaded). As far as I can work out, in 16.07 the "src" location is generated from templates/webapps/galaxy/galaxy.masthead.mako, but takes its value from the 'logo_src' parameter that is set in lib/galaxy/managers/configuration.py: ... # TODO: this doesn't seem right 'logo_url' : lambda i, k, **c: self.url_for( i.get( k, '/' ) ), 'logo_src' : lambda i, k, **c: self.url_for( '/static/images/galaxyIcon_noText.png' ), ... However I have no idea how to try and fix it - presumably it needs to incorporate the proxy-prefix setting somehow. (Btw the 'logo_url' does seem to point to the correct location however.) Can someone suggest a fix? Thanks Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Error when "Export History to File"
by D K 07 Dec '16

07 Dec '16

Hi galaxy-devs, I get an "Internal Server Error" when trying to "Export History to File". I get the following in my paster.log file: > .... Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no > attribute 'execute' > File '/opt/galaxy/lib/galaxy/web/framework/middleware/error.py', line 151 > in __call__ > app_iter = self.application(environ, sr_checker) > File '/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', > line 85 in __call__ > return self.application(environ, start_response) > File > '/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', > line 640 in __call__ > return self.application(environ, start_response) > File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 135 in __call__ > return self.handle_request( environ, start_response ) > File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 194 in > handle_request > body = method( trans, **kwargs ) > File '/opt/galaxy/lib/galaxy/webapps/galaxy/controllers/history.py', line > 1260 in export_archive > self.queue_history_export( trans, history, gzip=gzip, > include_hidden=include_hidden, include_deleted=include_deleted ) > File '/opt/galaxy/lib/galaxy/web/base/controller.py', line 393 in > queue_history_export > history_exp_tool.execute( trans, incoming=params, history=history, > set_output_hid=True ) > AttributeError: 'NoneType' object has no attribute 'execute' > > CGI Variables > ------------- > CONTENT_LENGTH: '0' > HTTP_ACCEPT: > 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' > HTTP_ACCEPT_ENCODING: 'gzip, deflate, sdch' > HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8,fr;q=0.6' > HTTP_CONNECTION: 'keep-alive' > HTTP_COOKIE: > 'galaxysession=c6ca0ddb55be603a84da157bd892a9e699b161141ab9ce96d24ae4db9c34333de097bd8cf0510125; > SAPPORTALSDB0=urn%253Acom.sapportals.portal%253Adsm%2526debug%3D*; > SAPWP_active=1; > SMSESSION=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...17118.1452298948' > HTTP_HOST: 'xxx.com:8080' > HTTP_REFERER: 'xxx.com:8080/galaxy' > HTTP_UPGRADE_INSECURE_REQUESTS: '1' > HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 > (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36' > PATH_INFO: '/history/export_archive' > QUERY_STRING: 'preview=True' > REMOTE_ADDR: '10.20.52.124' > REQUEST_METHOD: 'GET' > SCRIPT_NAME: '/galaxy' > SERVER_NAME: '0.0.0.0' > SERVER_PORT: '8080' > SERVER_PROTOCOL: 'HTTP/1.1' > > WSGI Variables > -------------- > application: <paste.recursive.RecursiveMiddleware object at 0xc88eb50> > controller_action_key: u'web.history.export_archive' > is_api_request: False > paste.cookies: (<SimpleCookie: > SAPPORTALSDB0='urn%253Acom.sapportals.portal%253Adsm%2526debug%3D*' > SAPWP_active='1' > SMSESSION='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...7118.1452298948') > paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] > paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object > at 0xc88ead0> > paste.httpserver.proxy.host: 'dummy' > paste.httpserver.proxy.scheme: 'http' > paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at > 0xb8ae210> > paste.parsed_querystring: ([('preview', 'True')], 'preview=True') > paste.recursive.forward: <paste.recursive.Forwarder from /galaxy> > paste.recursive.include: <paste.recursive.Includer from /galaxy> > paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from > /galaxy> > paste.recursive.script_name: '/galaxy' > paste.throw_errors: True > request_id: '6abfe982bc1011e69fd4005056ab0b73' > webob._parsed_query_vars: (GET([(u'preview', u'True')]), 'preview=True') > wsgi process: 'Multithreaded' > ------------------------------------------------------------

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December Galaxy News: New web site, GAMe deadline extended
by Dave Clements 06 Dec '16

06 Dec '16

Hello all, The *December Galaxy News <https://new.galaxyproject.org/GalaxyUpdates/2016_12/>* is hot off the press, *and is was produced on a a hot new press. *Highlights this month include: - The *Galaxy Community Hub (the Hub) <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-community-hub-t…>* will be the new home for Galaxy Community documentation, replacing the current wiki. - And we are asking for help to get it ready for it's official launch <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#the-community-hub-cont…> - *Galaxy Australasia Meeting (GAMe 2017) <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-australasia-mee…>*: February 3-9, Melbourne, Victoria, Australia. - *Talk abstract submission extended to 14 December.* - *Early registration ends 31 December.* - And of course, other upcoming events <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#all-upcoming-events> too There are also 60 new publications (including eight featured pubs), four open positions, two new public Galaxy servers, new releases of Planemo & Pulsar, and other news too. Dave Clements and the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy Orione server name
by Blaise Pascal Bougnom 06 Dec '16

06 Dec '16

Dear, Please you give me the server name of Galaxy Orione?, It is to upload my file via FTP. Best wishes Dr Blaise Bougnom b.p.bougnom(a)bham.ac.uk<mailto:R.Huynh@bham.ac.uk> [cid:image001.jpg@01CDC96B.45E56E80] Antimicrobials Agents Research Group Institute of Microbiology and Infection Room S110, Biosciences Building Edgbaston Birmingham B15 2TT Tel: 012141 58693 Mob: 075031 65000

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ToolShed devteam tools error
by Yip, Miu ki 05 Dec '16

05 Dec '16

Hi all, After installing the following devteam tools from the ToolShed: Base Coverage/Cluster/Complement/Concatenate/Flanking_features/get_flanks/Intersect/Join/Merge/Subtract The tools give an error after being run. Traceback (most recent call last): File "/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/0a3e3133b09d/basecoverage/gops_basecoverage.py", line 15, in <module> from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped File "/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 18, in <module> from mako.template import Template ImportError: No module named mako.template Both the python virtual environment and the machine locally has the module mako installed. This module is also accessible via the interactive python shell. Is the error coming from the galaxy.tools.util.galaxyops or something else? Thanks! Miuki

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Galaxy 16.07: datasets don't update to yellow "running" state with novel job runner
by Peter Briggs 05 Dec '16

05 Dec '16

Dear Galaxy devs (Apologies: this is a repost of my message from last week, with a correction: the problem actually appears in the current Galaxy release 16.07.) I've recently updated our local Galaxy instances to use a novel in-house job runner (as part of a migration to a new VM platform). In all versions of Galaxy pre-16.07, the runner executes without any problems. However in 16.07 there is a minor bug in the UI, where jobs never update from the grey "queued" state to the yellow "running" state. The jobs themselves run okay in all versions. Does anyone know if there were changes in 16.07 which might have caused this? I couldn't see anything in the change log, or by comparing with the distributed runners. (The our runner code can be seen here: https://github.com/pjbriggs/ansible-palfinder-galaxy/blob/jse-drop-add-pref… with the implementation of the 'check_watched_item' method being the likely culprit?) Any suggestions immensely appreciated! Best wishes Peter ________________________________________ From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of Peter Briggs [peter.briggs(a)manchester.ac.uk] Sent: Friday, December 02, 2016 2:58 PM To: galaxy-dev(a)lists.galaxyproject.org Subject: [galaxy-dev] Datasets no longer automatically update to yellow "running" state using novel job runner Hello all I've recently updated our local Galaxy instances to use a novel in-house job runner as part of a migration to a new VM platform. As far as I can determine the runner is able to run jobs without any issues, on all versions of Galaxy that I've tried (v15.10/v16.01/v16.04/release_16.10). However: when moving to release_16.10 I've noticed a minor issue with the UI, where the job state in the history no longer automatically switches from the grey "queued" state to the yellow "running" state - even though the logs indicate that the job status has changed internally. Refreshing the history correctly updates the job to the correct yellow "running" state (so it would seem that internally Galaxy knows that the job status has changed), and transitions between other states seem to happen automatically. Comparing my novel runner code with that for e.g. the drmaa runner , I can't see what might be missing from mine to cause this issue. I had wondered if it could be a problem with out of date Javascript in the UI somehow not detecting the job status change from "queued" to "running", but using the "local" job runner doesn't exhibit this behaviour. (The source code for the runner can be found here: https://github.com/pjbriggs/ansible-palfinder-galaxy/blob/jse-drop-add-pref… It submits jobs to the cluster by "dropping" the scripts into a shared directory, which are then collected and executed by a separate process running on the cluster - with all communication done via files.) Can anyone suggest what might be happening to cause this issue? Many thanks Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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galaxy-dev December 2016