galaxy-dev June 2017

galaxy-dev@lists.galaxyproject.org

34 participants
27 discussions

Mac OS X, edgeR installtion
by Bongsoo Park 20 Jun '17

20 Jun '17

Hi All, I faced a problem in edgeR execution. My test environment is MacOS X, R version 3.3.2. Error message: Fatal error: Matched on Execution halted Error: package ‘limma’ was built for x86_64-apple-darwin14.5.0 Execution halted Anyone has the sample problem? Thanks in advance. Bongsoo

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Singularity Container forks ?
by Nikos Nikoloutsakos 20 Jun '17

20 Jun '17

Hello, Are there any galaxy forks using Singularity images instead of Docker ? Is it trivial enough to replace "docker run" with "singularity exec" ? Thank you, Nikos -- Nikos Nikoloutsakos Greek Research and Technology Network (GRNET) ☎ +30 210 7471127 ✉ nikoloutsa(a)grnet.gr hpc.grnet.gr

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Admin Training Poll: Where should Galaxy Admin Training be held next?
by Dave Clements 19 Jun '17

19 Jun '17

*Give us your input! <http://bit.ly/gatpoll>* Hello all, Last November the Galaxy Project offered it's first ever week-long Galaxy Admin Training. It was offered in Salt Lake City and drew ~35 participants from all over the world. The material was presented again at another training at the Galaxy Australasia Meeting <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> in February 2017. For the coming year the project (and other groups) are interested in offering it again. *We would like your input <http://localhost:8080/news/2017-06-admin-training-poll/(http://bit.ly/gatpo…>* to help us to decide where to offer this training again during the coming year. Please respond <http://bit.ly/gatpoll> by Friday, June 23. Thanks, Dave C on behalf of Your friendly Galaxy Admin Trainer Community -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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Re: [galaxy-dev] AD Intergration
by Matthias Bernt 16 Jun '17

16 Jun '17

Hi Jelle, I just (in this very moment) solved the "option error" issue for our galaxy installation. see my comment on the first issue mentioned by john: https://github.com/galaxyproject/galaxy/issues/3178#issuecomment-306538866 Maybe you do not need to compile everything from source (as I needed to). Best, Matthias

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drmaa resubmission
by Matthias Bernt 16 Jun '17

16 Jun '17

Dear list, I was thinking about implementing the job resubmission feature for drmaa. I hope that I can simplify the job configuration for our installation (and probably others as well) by escalating through different queues (or ressource limits). Thereby I hope to reduce the number of special cases that I need to take care. I was wondering if there are others - who are also interested in this feature and want to join? I would try to give this project a head start in the next week. - that may have started to work on this feature or just started to think about it and want to share code/experience Best, Matthias

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drmaa job status
by Matthias Bernt 16 Jun '17

16 Jun '17

Dear list, I have two question for all DRMAA users. Here is the first one. I was checking how our queuing system (univa GridEngine) and Galaxy react if jobs are submitted that exceed run time or memory limits. I found out that the python drmaa library cannot query the job status after the job is finished (for both successful and unsuccessful jobs). In lib/galaxy/jobs/runners/drmaa.py the call gives an exception self.ds.job_status( external_job_id ) Is this always the case? Or might this be a problem with our GridEngine? I have attached some code for testing. Here the first call to s.jobStatus(jobid) works, but the second after s.wait(...) doesn't. But I get "drmaa.errors.InvalidJobException: code 18: The job specified by the 'jobid' does not exist." The same error pops up in the Galaxy logs. The consequence is that jobs that reached the limits are shown as completed successfully in Galaxy. Interestingly, quite a bit of information can be obtained from the return value of s.wait. I was wondering if this can be used to differentiate successful from failed jobs. In particular hasExited, hasSignal, and terminateSignal are different in the two cases. Cheers, Matthias

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Re: [galaxy-dev] AD Intergration
by Hans-Rudolf Hotz 16 Jun '17

16 Jun '17

always keep the mailing list in the loop! in order for others to help or learn On 06/08/2017 07:27 PM, John Chen wrote: > Hans-Rudolf > > This is the error I get when I start the Galaxy server. > ... > xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105 > This is very informative. Looking at line 8 in your file: <server><a class="moz-txt-link-freetext" href="ldap://ldap.xxx.xx">ldap://ldap.xxx.xx</server> The element "a" is not terminated What happens, if you try just <server>ldap://ldap.xxx.xx</server> Regards, Hans-Rudolf

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Galaxy slurm error
by evan clark 15 Jun '17

15 Jun '17

Has anyone ever encountered an error such as this when running galaxy with slurm and submitting files for upload and unzip. slurmstepd: get_exit_code task 0 died by signal

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Galaxy Job Error
by evan clark 14 Jun '17

14 Jun '17

Has anyone seen a similar error like this before. We are unsure if galaxy is causing the issue or it is being cuased by slurm as it seems galaxy is prematurely deleting a file. galaxy.jobs.runners DEBUG 2017-06-14 19:36:45,719 (3261/143577) Unable to cleanup /cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec: [Errno 2] No such file or directory: '/cm/shared/apps/galaxy/prod/galaxy/database/jobs_directory/003/3261/galaxy_3261.ec' galaxy.jobs.output_checker DEBUG 2017-06-14 19:36:45,725 Tool produced standard error failing job - [slurmstepd: get_exit_code task 0 died by signal

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Release of Galaxy 17.05
by Jennifer Hillman-Jackson 12 Jun '17

12 Jun '17

Dear Galaxy Fans, We are pleased to announce the *release of Galaxy 17.05*. Thanks to the #usegalaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/master/releases/17.05_announce.html Highlights: *Tag your data with propagating hashtags* Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships. These two movies (both under a minute) explain how to use this with datasets <https://vimeo.com/216884518> and with collections <https://vimeo.com/216895965>. Learn more about Galaxy histories in our updated tutorial <https://galaxyproject.org/tutorials/histories/> *Drag & Drop datasets into tool inputs*Interface now allows dragging datasets from history panel into the content selectors of the tool form. Implemented in Pull Request 3871 <https://github.com/galaxyproject/galaxy/pull/3871>.*Upload directly to a collection* You can now bypass the history manipulation and upload your data straight into a collection for convenience. Learn more about collections and how to use them in a new tutorial <https://galaxyproject.org/tutorials/collections/>. We extend special thanks to the 64 New Contributors <https://docs.galaxyproject.org/en/master/releases/17.05_announce.html#new-c…> to Galaxy in the past year. *Thanks for using Galaxy!* *http://galaxyproject.org <http://galaxyproject.org>*

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galaxy-dev June 2017