- galaxy-dev - lists.galaxyproject.org

ImportError and Project life cycle
by Matthias Bernt 17 Feb '17

17 Feb '17

Dear galaxy-dev list, I'm currently trying to introduce myself to the galaxy server, i.e., learning how to use and administer a galaxy server. I have installed galaxy following this excellent tutorial: https://github.com/martenson/dagobah-training Then I tried the tool "FASTQ Quality Trimmer by sliding window" which is mentioned in NGS101-6 tutorial. I installed the tool from tool shed, but I get a python error (the Admin panel shows that all dependencies are installed): Traceback (most recent call last): File "/home/berntm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py", line 3, in <module> from galaxy_utils.sequence.fastq import fastqReader, fastqWriter File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7, in <module> from six import Iterator, string_types ImportError: No module named six Do you have an idea what could be wrong? I guess that this is to little information, but I did not know which kind of additional information would be helpful. Another question: At my institution quite a lot of NGS projects are carried out. After a project is finished all methods and data are stored to a long term read only tape archive. For the future the idea is to use galaxy. Which options are there to implement such a project life cycle with galaxy? A last general question: would it be better to send a separate mail to the list when I have multiple questions? Best regards, Matthias Bernt

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GalaxyAdmins meetup starting soon
by Enis Afgan 16 Feb '17

16 Feb '17

Hello again, This month's GalaxyAdmins call with start in just a bit over an hour. We will be taking a look at the all-new CloudLaunch application ( beta.launch.usegalaxy.org) with a live demo and an overview of the backend architecture. The call will be held using an online conference room <https://connect.johnshopkins.edu/gxyadmins201702/>, which will open 15 minutes before the meetup. More details about the content and access instructions are available here https://new.galaxyproject.org/community/galaxy-admins/meetups/2017-02-16/

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Bad UID exception with pbs_python on galaxy 16_10 and torque 6.02
by Vandeweyer Geert 16 Feb '17

16 Feb '17

Hi all, We've been running a galaxy server for the last few years successfully, using pbs_python for connection to our HPC. Recently, we've purchased a new system, and we're trying to install galaxy on it. However, we are having some issues. When we try to submit jobs, galaxy returns the following error: galaxy.jobs.runners.pbs WARNING 2017-02-15 16:55:22,178 (20) pbs_submit failed (try 1/5), PBS error 15025: Bad UID for job execution On the pbs_server, we see: 02/16/2017 09:14:43.631;128;PBS_Server.7156;Req;req_reject;Reject reply code=15025(Bad UID for job execution MSG=ruserok failed validating galaxyuser/galaxyuser from galaxy.uza.be), aux=0, type=QueueJob, from galaxyuser(a)galaxy.uza.be However, when we submit the generated qsub script manually, using the same user, queue and pbs_account (-A) settings, the job runs just fine. In our opinion this indicats an issue with galaxy somewhere. Running jobs locally also works. The docs state that we need to scramble a specific pbs_python version for our recent pbs version, but the mentioned files are missing in galaxy 16_10. Some information: ============= pbs_server version : 6.02 galaxy: v16_10 deprecated procedures: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster (in PBS : egss.ini and scripts/scramble.py are missing) Has anybody seen this before? Are there newer docs available on pbs_python ? Best, Geert

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GalaxyAdmins online meetup: this Thursday
by Enis Afgan 15 Feb '17

15 Feb '17

This is a reminder that we are going to have a GalaxyAdmins call really soon now! The talk will be held on Thursday Feb 16th at 11AM EST. See your local time here <http://bit.ly/2kPgfSF>. with the following topic being presented: CloudLaunch <https://beta.launch.usegalaxy.org/> is an application for launching Galaxy on the Cloud instances. In this talk, an all-new version will be presented. The new CloudLaunch (beta.launch.usegalaxy.org) allows multiple flavors of Galaxy to be deployed, Docker images or applications other than Galaxy. Each application can have its own custom user interface developed to accommodate the specific application needs, which will be demonstrated.

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Fwd: Galaxy on the Amazon cloud
by Jennifer Hillman-Jackson 15 Feb '17

15 Feb '17

---------- Forwarded message ---------- From: Матвей Спринджук <msprindzhuk(a)mail.ru> Date: Wed, Feb 15, 2017 at 1:01 AM Subject: Galaxy on the Amazon cloud Are there any guidelines and tutorials on how to tune Galaxy instance in the Amazon cloud environment? We need to know how to set up .ini and .xmls files in details. I have read all the documentation which is available. We have one fresh Galaxy instance at https://genomics.tbportal.org/galaxy/ and struggling on setting it up properly. Thank you and your Team Matvey Sprindzuk, computer/biomedical scientist, MD Belarus, Minsk, UIIP +375 29 567 10 73 <+375%2029%20567-10-73>

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nginx x-accel
by Briand, Sheldon (NRC/CNRC) 15 Feb '17

15 Feb '17

Hi, I have galaxy 16.10. Whenever I try to download a file now nothing happens. I have followed the configuration guide for nginx to allow it to handle file downloads. However the nginx logs show that the file path has /etc/nginx/htmlTrue in front of the correct path. Obviously I have a misconfiguration somewhere but I am not sure what the problem is. Could someone point me in the right direction? Thanks, -Sheldon Sheldon Briand Computer Systems and Applications Analyst National Research Council/Government of Canada Sheldon.briand(a)canada.ca/<mailto:Sheldon.briand@canada.ca/> Tel: (902) 426-1677

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Upgrade migration scripts
by Matthias Bernt 15 Feb '17

15 Feb '17

Der galaxy-dev list, I just updated my 16.10 installation to 17.01 in order to see how upgrading works. I followed https://wiki.galaxyproject.org/Admin/Maintenance where point 8 is to run migration scripts. Also the Admin Course (https://martenson.github.io/dagobah-training/10-upgrading-release/upgrading…) refers to tool and DB migration steps that need(?) to be invoked. I checked the output of run.sh and it seems to me that all migration scripts are run automatically: eg. there is output like: migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully ... So I was wondering what the admin should do here? Just check for errors or problems? Cheers, Matthias

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GalaxyAdmins online meetup: call details
by Enis Afgan 15 Feb '17

15 Feb '17

So you don't miss a single email in your inbox about the GalaxyAdmins call, I'm sending the second one. This one has the necessary call details info: The meetup's online conference room will open 15 minutes before the meetup. The call will use Johns Hopkins' Adobe Connect server <http://connect.johnshopkins.edu/welcome/>, which in turn uses Adobe Flash. You are encouraged to connect a few minutes early to work out any unexpected bumps. Complete connection details, including screenshots of the process are available on the event page: https://new.galaxyproject.org/community/galaxy-admins/meetups/2017-02-16/

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Galaxy Restart & Jobs finishing
by Yip, Miu ki 14 Feb '17

14 Feb '17

Hi all, Is there a way to restart Galaxy without having to wait till all the outstanding jobs are finished running? I’ve noticed that whenever Galaxy daemon is stopped and then started, the UI does not return back online until all the jobs that were running are finished or killed because they are all running on the same port as the original program. Is there a configuration that needs to be changed so that the application can restart right away without having to wait or kill jobs? Thanks!

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How to build a fresh Docker image from the latest Galaxy
by Md. Rezaul Karim 14 Feb '17

14 Feb '17

Hi there, I was wondering how to build a fresh Docker image/container from the latest version of Galaxy with all the tools available from the tool shed? Please note that I can build a Docker image for Galaxy by using the following Dockerfile: # VERSION 0.1 FROM bgruening/galaxy-stable:dev MAINTAINER Asif Karim<asif.karim.csedu"gmail.com> ENV GALAXY_CONFIG_BRAND BioOpener RUN curl -sL https://github.com/bgruening/galaxytools/archive/master.tar.gz | tar xz && cp -r galaxytools-master/visualisations/* config/plugins/visualizations/ && rm -rf ./galaxytools-master RUN install-biojs msa RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_pdf_api2_2_023" \ "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name infernal --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o biopython --name package_biopython_1_61 --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_trnascan_1_3_1 --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_aragorn_1_2_36 --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name trna_prediction --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o lionelguy --name rnammer --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name rnaz --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name blockclust --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name cofold --panel-section-name RNATools" RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_vienna_rna_1_8" \ "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name package_bowtie_0_12_7" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name vienna_rna --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_squid_1_9g " \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_randfold_2_0 " \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_mapper --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_quantifier --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2 --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnashapes --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name suite_mirdeep_2_0" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name antarna --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name dorina --panel-section-id getext" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name compalignp --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnabob --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mafft --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnacode --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name gotohscan --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name kinwalker --panel-section-name RNATools" RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mea --panel-section-name RNATools" \ "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name sortmerna --panel-section-name RNATools" The Docker image works fine on my machine. However, I'm not sure if I image is built with the latest features of Galaxy. My second question is can I specify non-shed tools while building the Galaxy Docker image? Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc PhD 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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