Proper Galaxy Installation

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Proper Galaxy Installation

Durdevic, Marija

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: [hidden email]

Email: [hidden email]

 

Web: https://zmf.medunigraz.at/

 


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Re: Proper Galaxy Installation

Sebastian Schaaf
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 As SLES is hopelessly outdated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: [hidden email]
> Email: [hidden email]
>
> 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/



___________________________________________________________
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/
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Re: Proper Galaxy Installation

Durdevic, Marija
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:[hidden email]]
Sent: Monday, May 09, 2016 2:27 PM
To: Durdevic, Marija
Cc: [hidden email]
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: [hidden email]
> Email: [hidden email]
>
> 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/



___________________________________________________________
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/