- galaxy-dev - lists.galaxyproject.org

How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?
by Md. Rezaul Karim 23 Jun '17

23 Jun '17

Dear All, I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/. <http://bioopenergalaxy.insight-centre.org/> However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file: # This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp # This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org Any help or pointer would be highly appreciated. Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>

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dexseq pysam error
by Rui Wang 21 Jun '17

21 Jun '17

Hi Folks, I got the galaxy docker image and played with it. However, I keep getting this when I use dexseq: Fatal error: Exit code 1 () Could not import pysam, which is needed to process BAM file (though not to process text SAM files). Please install the 'pysam' library from https://code.google.com/p/pysam/ Looks like there is a conda env that is built on the fly and it doesn't have some dependencies installed. If I do the following biocLite("DEXSeq") inside the conda-env, then pysam is imported properly. Seems it installs the dexseq 1.22. I looked at the package in /tool_deps/_conda/ __bioconductor-dexseq(a)1.20.1, it's 1.20.1 as the name says. I'm not sure how this could be fixed...my thought would be update the conda env dependency to include dexseq 1.22 not 1.20, but I'm not familiar with conda...Could someone give me a hand? :-) Thanks, Rui

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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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