Proper Galaxy Installation
Dear all, I am currently working on Galaxy installation at our Center for Medical Research. As a login server, we are using VM based on SLES-12. We are planning to extend it on a Cluster later and we would like to use SLURM as DRM. Is there any recommendation or "step-by-step" recipe how to setup Galaxy in a proper way to avoid future issues? Are they any recommendation regarding the filesystem of directory management system that I should care about in advance? Any advice from experienced developers will be more than helpful. Thank you in advance. Regards, Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic@medunigraz.at Email: marija.djurdjevic@klinikum-graz.at Web: https://zmf.medunigraz.at/
Dear Marija, I would recommend to google for the "ngs-fablab" - there are two posters and a talk online from the GCCs 2014 and 2015, respectively. I admit, it may look like self-advertising :). But in fact we set up a local instance at the medical faculty in Munich (LMU) which is quite similar to yours in terms of pre-conditions: we (have to) deal with SLES 11, do virtualization (although via vSphere, SLES just for the guests) and intended to go modular, step by step, including cluster usage. As we had to rely on our own hardware exclusively and clean system setups where necessary repetively, we created a setup framework that configures servers remotely for being Galaxy host, fileserver, cluster head/node or arbitrary combinations. You just need a blank SLES (we tested also other UNIXes like Ubuntu and CentOS) and SSH enabled. As SLES is hopelessly outdated regarding software packages, everything is compiled from source. The framework's technical base is Ansible, which has become quite well known also in other parts of the Galaxy community (initially introduced by the core team). If you like to contact us feel free - we are curious for others in the medical field :). Cheers, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499
Dear all,
I am currently working on Galaxy installation at our Center for Medical Research. As a login server, we are using VM based on SLES-12. We are planning to extend it on a Cluster later and we would like to use SLURM as DRM. Is there any recommendation or "step-by-step" recipe how to setup Galaxy in a proper way to avoid future issues? Are they any recommendation regarding the filesystem of directory management system that I should care about in advance? Any advice from experienced developers will be more than helpful. Thank you in advance. Regards,
Mag. Marija Ðurðeviæ Core Facility Computational Bioanalytics
Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria
Phone: +43 316/385-73024 Fax:+43 316/385-73009
Email: marija.djurdjevic@medunigraz.at Email: marija.djurdjevic@klinikum-graz.at
Web: https://zmf.medunigraz.at/
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Dear Sebastian, Thank you very much for your response. I just had a look at posters few minutes before I receive your email. It looks really great and helpful. I think it will save me a lot of time during Galaxy installation. Thank you once again. Regards, Marija -----Original Message----- From: Sebastian Schaaf [mailto:schaaf@ibe.med.uni-muenchen.de] Sent: Monday, May 09, 2016 2:27 PM To: Durdevic, Marija Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Proper Galaxy Installation Dear Marija, I would recommend to google for the "ngs-fablab" - there are two posters and a talk online from the GCCs 2014 and 2015, respectively. I admit, it may look like self-advertising :). But in fact we set up a local instance at the medical faculty in Munich (LMU) which is quite similar to yours in terms of pre-conditions: we (have to) deal with SLES 11, do virtualization (although via vSphere, SLES just for the guests) and intended to go modular, step by step, including cluster usage. As we had to rely on our own hardware exclusively and clean system setups where necessary repetively, we created a setup framework that configures servers remotely for being Galaxy host, fileserver, cluster head/node or arbitrary combinations. You just need a blank SLES (we tested also other UNIXes like Ubuntu and CentOS) and SSH enabled. As SLES is hopelessly outdated regarding software packages, everything is compiled from source. The framework's technical base is Ansible, which has become quite well known also in other parts of the Galaxy community (initially introduced by the core team). If you like to contact us feel free - we are curious for others in the medical field :). Cheers, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499
Dear all,
I am currently working on Galaxy installation at our Center for Medical Research. As a login server, we are using VM based on SLES-12. We are planning to extend it on a Cluster later and we would like to use SLURM as DRM. Is there any recommendation or "step-by-step" recipe how to setup Galaxy in a proper way to avoid future issues? Are they any recommendation regarding the filesystem of directory management system that I should care about in advance? Any advice from experienced developers will be more than helpful. Thank you in advance. Regards,
Mag. Marija Ðurðeviæ Core Facility Computational Bioanalytics
Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria
Phone: +43 316/385-73024 Fax:+43 316/385-73009
Email: marija.djurdjevic@medunigraz.at Email: marija.djurdjevic@klinikum-graz.at
Web: https://zmf.medunigraz.at/
___________________________________________________________ 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/mailinglists/
participants (2)
-
Durdevic, Marija -
Sebastian Schaaf