July 2017 - galaxy-dev - lists.galaxyproject.org

"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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