- galaxy-dev - lists.galaxyproject.org

specify file_path for each Galaxy registered users
by Weiyan Shen 05 May '14

05 May '14

Galaxy developers: We can set the file_path in universe_wsgi.ini to specify the saved Galaxy results.But whether it is possible for us to specify file_path for each Galaxy registered users,for which multi-hard disks can be used effectively in some ways? Thank you very much for any help. Regards,Weiyan

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display_at_callback
by David Hoover 02 May '14

02 May '14

What is the display_at_callback configuration setting, and how does it work? Can it be used as a workaround for remotely authenticated instances of galaxy? David Hoover Helix Systems Staff NIH

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Cleanest way to disable job-runs during a long cluster maintenace window?
by Curtis Hendrickson (Campus) 01 May '14

01 May '14

Folks The cluster under our galaxy server will be down for a WEEK, so it can be relocated. The fileserver that hosts the galaxy datasets, the galaxy server and the galaxy database will stay up. What's the most elegant way to disable people's ability to run new jobs, without blocking them from browsing existing histories and downloading/viewing their data? Our configuration: External Auth universe_wsgi.ini:use_remote_user = True Job runner: SGE universe_wsgi.ini:start_job_runners = drmaa and the new_file_path and job_working_directories are on a fileserver that will be down. grep -H /scratch/share/galaxy universe_wsgi.ini universe_wsgi.ini:file_path = /scratch/share/galaxy/staging # available universe_wsgi.ini:new_file_path = /scratch/share/galaxy/temp # down universe_wsgi.ini:job_working_directory = /scratch/share/galaxy/job_working_directory # down We'd rather something nicer than just letting the jobs go to the queue and never get run. Regards, Curtis

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Globus tools for galaxy
by David Hoover 01 May '14

01 May '14

Are there any tools available for transferring files using Globus? There’s nothing in the toolsheds, but there was a lot of chatter a few years ago. David Hoover Helix Systems Staff

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Help with cluster setup
by Jurgens de Bruin 01 May '14

01 May '14

Hi, This is my first Galaxy installation setup so apologies for stupid questions. I am setting up Galaxy on a Cluster running Torque as the resource manager. I am working through the documentation but I am unclear on some things: Firstly I am unable to find : *start_job_runners *within the universe_wsgi.ini and I dont want to just add this anywhere - any help on this would be create. Further more this is my job_conf.xml : <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="hpc" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers> <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. <handler id="cn01"/> <handler id="cn02"/> </handlers> <destinations> <destination id="hpc" runner="drmaa"/> </destinations> </job_conf> Does this look meaning full, further more where to I set the additional server:<id> in the universe_wsgi.ini. As background the cluster has 13 compute nodes and a shared storage array that can be accessed by all nodes in the cluster. Thanks again -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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Re: [galaxy-dev] Galaxy Error Message
by Hans-Rudolf Hotz 01 May '14

01 May '14

"Please keep all replies on the list by using "reply all"" well, what happens if you run Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments Hans-Rudolf On 04/28/2014 03:32 PM, Bradley Belfiore wrote: > Thank you for your quick response, my command tag is: > <command> > interpreter="bash">Rscript_wrapper.sh > /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata > $pathwayid $species $output > </command> > > So I believe Im calling R via the Rscript_wrapper.sh? > > As far as the #!/bin/bash, not sure why I had that there, I took it out now. > thanks, > Bradley Belfiore > > > On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Brad > > I don't you are using R to execute your R script.... > > How do you call your R script, ie how does the command tag looks in > the tool definition file? > > Also, why do you have a "#!/bin/bash" at the beginning of your R script? > > > Regards, Hans-Rudolf > > > > > On 04/27/2014 09:50 PM, Bradley Belfiore wrote: > > I am new to galaxy and while trying to convert an R tool to a Galaxy > usable tool I keep getting: > /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: > syntax > error near unexpected token `(' > > /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: > `args=(commandArgs(TRUE))' > > > any help as to how to remedy this would be greatly appreciated. The > first couple lines of my .R file are > # > #!/bin/bash > args<-(commandArgs(TRUE)) > > Thanks, > Brad > > > _____________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/__search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/> > >

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purging deleted datasets
by Milad Bastami 01 May '14

01 May '14

Dear all,I have some unwanted datasets to remove but I need their main histories, so in galaxy I just deleted the unwanted datasets but not the histories. Then I tried to purge the deleted datasets with the following commands: python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -6 -r python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -3 -r and I saw the this error: /galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.Purged 0 datasetsFreed disk space: 0Elapsed time: 0.0748069286346 Unfortunately I can't understand the warning and why nothing was deleted. Any help would be most appreciated.

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Problem with the "set_library_permissions" function on bioblend
by Kevin Muret 30 Apr '14

30 Apr '14

Hello to all, In recent days, I try to do the "set_library_permissions ()" bioblend's function working. I tried the following syntaxes, and it was unsuccessful. Anybody know how to use it? Or otherwise,how would it be possible to modify user access to libraries (or contents)? ---------------------------------------------- Bonjour à tous, Depuis quelques jours, je tente de faire fonctionner la fonction "set_library_permissions()". J'ai tenté les syntaxes suivantes, et ce fût sans succès. Quelqu'un saurait-il comment l'utiliser ? Ou comment serait-il possible de modifier les accès utilisateurs d'une autre manière ? ---------------------------------------------- "instance" is opened with an admin API key. 1 --> print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=None, modify_in=None, add_in=None, manage_in=None) Traceback (most recent call last): File "Workflow_Lib/work_test.py", line 76, in <module> main() File "Workflow_Lib/work_test.py", line 39, in main print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=None, modify_in=None, add_in=None, manage_in=None) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxy/libraries/__init__.py", line 308, in set_library_permissions return Client._post(self, payload, url=url) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxy/client.py", line 181, in _post r = self.gi.make_post_request(url, payload=payload, files_attached=files_attached) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxyclient.py", line 99, in make_post_request r.status_code, body=r.text) # @see self.body for HTTP response body bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> 2 --> print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=[admin_id], modify_in=[admin_id], add_in=[admin_id], manage_in=[admin_id]) 3 --> Moreover,are we supposed to view the content of this page?http://localhost:8080/api/libraries/417e33144b294c21/permissions ---------------------------------------------- Thank you in advance to the community for your help, Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform

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May 2014 Galaxy News Update
by Dave Clements 30 Apr '14

30 Apr '14

Hello all, The May 2014 Galaxy Update Newsletter<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05> is out! There's a lot going on in the project and the community right now. The big news in the past month is the move from the Galaxy-User mailing list to Galaxy Biostar<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Biostar> for user support. This has been running for a week now, and has been very well received. The other big news is upcoming events. *Early registration for GCC2013 closes May 23 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#GCC2014:_June_30_-_Jul…>* . Register now <https://wiki.galaxyproject.org/Events/GCC2014/Register> and save more than 70% on registration costs, and Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> registration is an additional 55% off if you register for both at the same time. We are also pleased to announce this year's keynote speaker<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Keynote_Speaker:_Steve…> and the first ever GCC Hackathon<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Hackathon_at_GC…> . There's also a Galaxy UK Tour<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#UK_May_2014_Galaxy_Tour> which is visiting Norwich and Edinburgh in May, and there are at least 17 other Galaxy related events<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Other_Events> in the next 70 days in Norway, France, *online*, Croatia, Thailand, Canada, the US, the Netherlands, and Australia As always, there are new papers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Papers> (47 of them, including four we highlighted), new public Galaxy Servers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Servers> (Globus Genomics Proteomics<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Globus_Genomics_Proteo…> and SunLab Galaxy<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#SunLab> ), new jobs<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Who.27s_Hiring> (7 postings in 6 countries), new tools in the project ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Project_ToolShe…> (um, *lots*), and a new public ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Tool_Sheds> (at the Dutch Techcentre for Life Sciences (DTL) <http://www.dtls.nl/dtl/>. Dave Clements and the Galaxy Team<https://wiki.galaxyproject.org/GalaxyTeam> http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Test ToolShed package_samtools_0_1_19 status error?
by Peter Cock 29 Apr '14

29 Apr '14

Hi all, I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:*13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies* - installation of these additional repositories is required* Tool shedNameOwnerChangeset revision testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939

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