galaxy-dev July 2017

galaxy-dev@lists.galaxyproject.org

33 participants
34 discussions

"Best practice" for maintaining genome list in Galaxy
by Peter van Heusden 06 Jul '17

06 Jul '17

Hi there Is there current "best practice" for maintaining a collection of reference genome data in a Galaxy server? I.e. filling in the dbkeys.loc and all_fasta.loc table and associated data. I know of the following discussions on this topic: 1. The data integration page: https://galaxyproject.org/admin/data-integration/ 2. The data managers page: https://galaxyproject.org/admin/tools/data-managers/ 3. This biostars answer: https://biostar.usegalaxy.org/p/7176/ 4. This page on custom genomes that seems to be user / history oriented: https://galaxyproject.org/learn/custom-genomes/ 5. This page on rsyncing from the Galaxy reference data collection: https://galaxyproject.org/admin/use-galaxy-rsync/ - quick test gives me rsync error though 6. This guide to using the human reference data: https://biostar.usegalaxy.org/p/14777/ 7. I hear the usegalaxy.org reference collection is available via cvmfs - I think this was discussed in a Galaxy Admins meetup at some point. None of this is comprehensive. There are 2 sets of questions for me (in my role as Galaxy admin): 1. If I want to make reference genomes and common indices (like for HISAT and BWA) available for e.g. human and mouse, what is the best way to do this? 2. If I want to add a genome for a non-model organism (e.g. M. tuberculosis or L. calcarifer) available, what is the best way to do this? Which data manager should or could I use? Thanks, Peter

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Moving Shared Data Library Folders
by D K 06 Jul '17

06 Jul '17

Is it possible to move the file locations of Shared data libraries that have already been added to the system? I just tried moving some of these files to a new location (e.g. /somewhere/files to /somewhere_else/libraries) and updating the galaxy.ini entry to point to the new location. However, files previously added to a library still point to the old location. I found this question on biostars: https://biostar.usegalaxy.org/p/1119/ Is the only way to do this sort of update to manually change such entries in the database? 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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conda problem with R libraries
by Jochen Bick 04 Jul '17

04 Jul '17

Hi all, I'm testing a tool with planemo and the conda dependencies are not running: <requirements> <requirement type="package" version="3.3.2">r-base</requirement> <requirement type="package" version="0.4.1">r-ggfortify</requirement> <requirement type="package" version="0.1.0">r-getoptlong</requirement> </requirements> galaxy.jobs.handler INFO 2017-07-04 13:11:42,935 (2) Job dispatched galaxy.util.object_wrapper WARNING 2017-07-04 13:11:43,062 Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases ...The following specifications were found to be in conflict: - cairo 1.14.6 4 - r-assertthat (target=r-assertthat-0.1-r3.3.2_4.tar.bz2) -> r-base 3.3.2* ... ... somehow the conflicts can not be resolved=? Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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galaxy-dev July 2017