June 2015 - galaxy-dev - lists.galaxyproject.org

GalaxyAdmins Online Meetup this Thursday: Peter Briggs on Galactic Engineering at Manchester
by Dave Clements 18 Jun '15

18 Jun '15

Hello all, The June 2015 online GalaxyAdmins meetup <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_06_18> will be this Thursday, 18 June, at 5pm Central European Time (see your local time <http://bit.ly/1F7zN8l>). Peter Briggs <http://galacticengineer.blogspot.co.uk/> of the University of Manchester <http://www.manchester.ac.uk/> and author of the *Galactic Engineer <http://galacticengineer.blogspot.co.uk/>* blog will talk about his Galaxy work deploying Galaxy and developing tools within the Bioinformatics Core Facility <http://www.ls.manchester.ac.uk/research/facilities/#bioinf> at the University of Manchester. John Chilton <https://wiki.galaxyproject.org/JohnChilton> will also give an update on recent and upcoming work on Planemo <https://github.com/galaxyproject/planemo>, a set of command-line utilities to assist in building and publishing Galaxy tools. We'll also discuss the upcoming GalaxyAdmins meetup, and the hackathons at GCC2015 <http://gcc2015.tsl.ac.uk/>. We'll post a link on the meetup page <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_06_18> on Thursday. Hope to see/hear you on Thursday, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Adding packages for bedtools and ucsc-utils for Trackster?
by Peter van Heusden 18 Jun '15

18 Jun '15

Hi there I'm trying to visualise some of our genome data using Trackster. Initial input is 790,000 lines of GFF3. When I try and create the visualisation, I get errors from two tools: Convert GFF to Interval Index on data 3 -- an out of memory error - I'll try and fix this by upping the memory limit for our Galaxy jobs Convert BED, GFF, or VCF to BigWig on data 3 -- bedtools and bedGraphToBigWig not found errors. I tried to resolve these by installing the ucsc-tools and bedtools packages - and they did install correctly - but I still get these file not found errors. Any idea how to fix this second problem? Thanks! Peter P.S. as an alternative to Trackster, does anyone have Galaxy interfaced to JBrowse?

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functional tests / database lock
by Ryan G 17 Jun '15

17 Jun '15

Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow? galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - <class 'sqlalchemy.exc.OperationalError'>: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef74… File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)

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Re: [galaxy-dev] Galaxy admin access
by Dannon Baker 17 Jun '15

17 Jun '15

Where are you executing this? You'll need to be in the galaxy/config directory, where galaxy.ini.sample exists. I'm looping the mailing list back in on this so other people might also be able to help. On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha <ADAVENP3(a)gru.edu> wrote: > When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no > such file or directory > > > -------- Original message -------- > From: Dannon Baker <dannon.baker(a)gmail.com> > Date: 06/15/2015 3:14 PM (GMT-05:00) > To: "Davenport, Aneisha" <ADAVENP3(a)gru.edu> > Subject: Re: [galaxy-dev] Galaxy admin access > > I'm not sure what you mean. You can edit the file using any text > editor, try 'nano', or emacs or vim if you're more comfortable with those. > > Does the file exist or not? If not, simply "cp galaxy.ini.sample > galaxy.ini" will do it. > > On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha <ADAVENP3(a)gru.edu> > wrote: > >> How do I create it and edit it on terminal? >> >> Aneisha Davenport >> ________________________________________ >> From: Dannon Baker [dannon.baker(a)gmail.com] >> Sent: Friday, June 12, 2015 9:44 PM >> To: Davenport, Aneisha; galaxy-dev(a)lists.galaxyproject.org >> Subject: Re: [galaxy-dev] Galaxy admin access >> >> Hi Aneisha, >> >> When you say you cannot alter config/galaxy.ini, what do you mean? You >> should be able to create (if not there) and edit this file in your regular >> terminal on that machine. >> >> Does a different user own the file, perhaps a 'galaxy' one? If so, you >> could change to that user and then edit. >> >> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha <ADAVENP3(a)gru.edu >> <mailto:ADAVENP3@gru.edu>> wrote: >> Hi, I work at the It service desk at the GRU Health and Science campus Ed >> Commons GB building and I have a customer trying to get admin access for >> the local installation of galaxy. We tried to follow the online >> instructions "In order to control your new Galaxy through the UI >> (installing tools, managing users, creating groups etc.) you have to become >> an administrator. First register as a new user and then give the user admin >> privileges like this: You add the Galaxy login ( email ) to the Galaxy >> configuration file (config/galaxy.ini). If the file does not exist you can >> copy it from the provided sample (config/galaxy.ini.sample). Note that you >> have to restart Galaxy after modifying the configuration for changes to >> take effect. >> >> >> # this should be a comma-separated list of valid Galaxy users >> admin_users = user1(a)example.com<mailto:user1@example.com>, >> user2(a)example.com<mailto:user2@example.com>" but we cannot alter the >> config/galaxy.ini file. Can you please give us assistance? Do you run in >> console or Terminal (this is a Macbook Air Laptop)? >> >> >> Aneisha Davenport >> ___________________________________________________________ >> 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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Bug in galaxy-dist/latest_15.05 for "Share history with user" function
by Peter Briggs 17 Jun '15

17 Jun '15

Hello I think a bug was introduced into galaxy-dist between the 15.03 and 15.05 releases, for the "Share history with user" function. The function works for 15.03 but fails in 15.05. To reproduce: 1. Click on the "cog" icon for a history and select "Share or publish" 2. Under "Share History with Individual Users" click "Share with a user" 3. Enter the email of another user on the system and click submit In 15.03 this returns to the sharing screen and indicates that the history has been shared with the specified user; in 15.05 this produces a stack trace (or "internal server error" in a production setting"). The following patch appears to fix the problem: diff -r c3cef260df88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py Fri May 15 15:20:17 2015 -0400 +++ b/lib/galaxy/webapps/galaxy/controllers/history.py Wed Jun 17 12:51:41 2015 +0100 @@ -899,7 +899,7 @@ for history_id in ids: history_id = self.decode_id( history_id ) history = self.history_manager.get_owned( history_id, trans.user, current_history=trans.history ) - histories.append( ) + histories.append( history ) return histories def _get_users( self, trans, user, emails_or_ids ): also available via this gist: https://gist.github.com/pjbriggs/65c29a87e094d4d257f6 Apologies if this has already been reported/fixed elsewhere, or if there's a better way to submit this fix (if so then please let me know) Best wishes 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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web interface says installation OK but log file says ERROR?
by Pablo Escobar 17 Jun '15

17 Jun '15

Hi all, I have installed "package_r_ggplot2_0_9_3" in my galaxy instance as dependency for "gatk2". The weird stuff is that in the web interface it says the installation completed correctly but in the galaxy log file I get many errors. As example, in the log file I get these errors: ERROR: this R is version 2.11.0, package 'stringr' requires R >= 2.14 Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'colorspac ERROR: this R is version 2.11.0, package 'ggplot2' requires R >= 2.14 installation of package 'reshape2_1.2.2.tar.gz' had non-zero exit status But at the end of the logfile I get this: tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,229 Changing status for tool dependency ggplot2 from Installing to Installed. tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,277 Tool dependency ggplot2 version 0.9.3 has been installed in /scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5. And in the webui it says the tool has been installed correctly (green). Is this normal? can I ignore the errors or I should worry about them? here you can see the complete log file when installing "package_r_ggplot2_0_9_3" https://gist.github.com/anonymous/3d5f73c019615c504964 thanks in advance for any advice. regards, Pablo.

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How to hide history and tool panel
by Makis Ladoukakis 17 Jun '15

17 Jun '15

Hi I was wandering how I can make the tool panel and history (left and right panels) to be hidden when the Galaxy instance starts. In the older versions you had to modify some .mako files but the newest setup has me a little confused. I'd appreciate any help. Kind regards, Efthymios Ladoukakis

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Repository installation error - missing
by Alexander Vowinkel 16 Jun '15

16 Jun '15

Hi, I have a custom tool_conf.xml in gbs_tools/gbs_tool_conf.xml It is added to the config and loaded without problems. "<toolbox tool_path="./gbs_tools">" But when I want to install tools from a toolshed (test and main) to it ("Shed tool configuration file"), it reports Error during installation. Clicking on the tool, it says "This repository is not installed correctly (see the Repository installation error below). [...]" But there is no "Repository installation error". So, how can I find out, what the problem is? Installing in the default tool_shed_conf.xml works. I also checked if it's a problem with the tool_path (I assume it points to the galaxy root). So I created a directory gbs_tools in gbs_tools, in case it is relative to the xml file directory. No difference. Thanks for help! Alexander

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config files in cloudman
by Alexander Vowinkel 16 Jun '15

16 Jun '15

Hi, the config/galaxy.ini is being overwritten when restarting Galaxy via the CloudMan Console. Unfortunately I can't find the file, that is used as template. I searched on the whole machine for "*.cloud", "galaxy.ini*" and "universe_wsgi.ini*". The only file I found was "/mnt/cm/installed_files/universe_wsgi.ini.cloud". Changes to this file doesn't have an effect. The corresponding bucket also doesn't contain this file. Where is this blueprint coming from? And where can I change it? I am using the next version of CloudMan (dev). I created an own instance with the Cloud Man playbook. Thanks a lot! Alexander

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minor visual bug found when using Firefox
by Ryan G 15 Jun '15

15 Jun '15

In the workflow editor, if you add an Input dataset collection, the "Collection Type:" shows list. No dropdown arrow appears using Firefox. A dropdown arrow appears when you mouse over using Chrome. In Firefox, if you mouse over where the dropdown box should be, you can still click to choose "list of datasets..." For the longest time, I thought this was broken until a co-worker showed me it works with Chrome. I'd make a Trello card for this but I can't access Trello from behind the company firewall....

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