galaxy-dev June 2017

galaxy-dev@lists.galaxyproject.org

34 participants
27 discussions

Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras 14 Mar '18

14 Mar '18

Dear Mohamed, Karim, galaxy-dev list, A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it... Wishing you a good week end. Cheers, Yvan -------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud(a)gmail.com> Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy +1 On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote: Dear all, I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy . Thanks in Advance, Mohamed ___________________________________________________________ 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/

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Groovy tool for galaxy
by Anshul Tak 22 Aug '17

22 Aug '17

Hi, I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found" So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed. Can you give me some pointers to solve this issue? -- With Regards, Anshul Tak

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Uncaught Error When Installing Tools From Toolshed
by William, Van Der Pol 24 Jul '17

24 Jul '17

Hello All, I have recently cloned and installed a clean version of Galaxy. I installed a tool from the toolshed and Galaxy says it is properly installed, however when I try to open the tool in the main page all I see is an "Uncaught Error" message. Does anyone have any ideas on what is causing this or at least how I can get a more telling error message? Thanks -Liam

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Issue with SLURM-DRMAA
by Dawes, Gwen 12 Jul '17

12 Jul '17

Hi folks, I just had a bit of an interesting problem with Galaxy. We have a configuration whereby work is submitted to our friendly local SLURM cluster via DRMAA. However, the PSNC base version is too old to be able to parse the more modern slurm configs, and was repeatedly failing to submit, stating that it was unable to parse slurm.conf. The updated version of this library by natefoo ( https://github.com/natefoo/slurm-drmaa ) using the multicluster branch works perfectly for submitting to a more modern SLURM, but this isn't referenced at the Admin/Config/Cluster page on galaxyproject.org . Can someone update this information? Thanks!

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DeepTools installation error
by Timo Janßen 05 Jul '17

05 Jul '17

Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as well for the dependencies, e.g. deeptools_bigwig_compare. I am currently using Galaxy 16.10 with nginx proxy. Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency: "Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433." Has anyone seen these problems before and knows a solution? Best regards, Timo Janßen -- ------------------------------------------------------------------------ Timo Janßen Wissenschaftliche Hilfskraft Arbeitsgruppe "Anwendungs- und Informationssysteme" Tel.: +49(0)551/201-1791 E-Mail: timo.janssen(a)gwdg.de ------------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG) Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau Sitz der Gesellschaft: Göttingen Registergericht: Göttingen, Handelsregister-Nr. B 598 ------------------------------------------------------------------------ Zertifiziert nach ISO 9001 ------------------------------------------------------------------------

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Python modules not found when starting with init system
by Maximilian Friedersdorff 28 Jun '17

28 Jun '17

Hi All, when my local galaxy is started using the init system (systemd on Ubuntu 16.04 in this instance). Some tools will fail, indicating that some python module do not exist. This is the result of uploading a 2KB plain text file: Traceback (most recent call last): File "/home/galaxy/galaxy/tools/data_source/upload.py", line 20, in <module> from galaxy.datatypes import sniff File "/home/galaxy/galaxy/lib/galaxy/datatypes/sniff.py", line 31, in <module> from galaxy.datatypes.binary import Binary File "/home/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 14, in <module> import pysam ImportError: No module named pysam Traceback (most recent call last): File "/home/galaxy/galaxy/database/jobs_directory/000/39/set_metadata_EI05GD.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 23, in <module> from sqlalchemy.orm import clear_mappers ImportError: No module named sqlalchemy.orm When the same galaxy install is started directly using the 'run.sh' script in the install directory, everything works fine. I've verified that I can manually import pysam and sqlalchemy.orm if I execute the python interpreter located at <install_dir>/.venv/bin/python directly. Any ideas? I've attached the init script. TL;DR Galaxy cannot import some python modules when started by the init system. No idea why. Galaxy version: 17.05 OS: Ubuntu 16.04 Many Thanks Max -------------------------------------------------------------------- Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd myfyrwyr. (Arolwg Cenedlaethol y Myfyrwyr 2016) www.aber.ac.uk Top 4 UK university and best in Wales for student satisfaction (National Student Survey 2016) www.aber.ac.uk

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new installation galaxy-17.05 - Uncaught error.
by Fernandez Edgar 26 Jun '17

26 Jun '17

Hey Guys, Hope everyone is doing ok. I have a small issue with a brand new installation of galaxy-1705. It starts properly and I installed some tools. But when I try to test any tools I get and "Uncaught error" (see picture). I can't find anywhere in the logs what is happening. Any ideas? Regards, Edgar Fernandez System Administrator (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568

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Galaxy Dinner @ ISMB/ECCB/BOSC 2017
by Dave Clements 25 Jun '17

25 Jun '17

Hello all, If you are interested in getting together for dinner at ISMB/ECCB/BOSC 2017 #BOSC2017 then please *let us know by Friday:* http://bit.ly/ismbdinnerpoll Thanks, Dave C -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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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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galaxy-dev June 2017