Re: Local Galaxy implimentation

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: Local Galaxy implimentation

Anton Nekrutenko
Lee:

I am CC'ing you e-mail to galaxy-dev list. You can get a lot of useful answers by posting to this list. Maintaining Galaxy is not different from maintaining other software resources. To run it locally you will need to have a system administration supervision as with any other high performance system. It is wonderful that you are sending your staff members to Galaxy Community Conference as they will be able to interact with key Galaxy Team members such as Nate Coraor, who runs Penn State instance here.

Thanks!

anton



On Feb 25, 2011, at 6:14 AM, Lee Hazelwood wrote:

> Dear Prof Nekrutenko,
>
> The university where I work is looking to locally implement your elegant software to enable us to view and analyse the rapidly growing amount of sequence data. We will be sending two staff members to the conference in Lunteren in May to get right into the detail on how we would achieve this.
>
> However, with all things I need to request some time/ support for running such a system in advance of May.
> If you could help by briefly answering the questions below I would much appreciate it.
>
> *   What is a realistic amount of someones time to implement Galaxy on a Linux  server so that it can be used by researchers using the Web?
> *   What is the usual time overhead to keep it running and how skilled would they have to be?
>
> I should say, this will be for local biological researchers only, approx 20-30 dealing in Exome and Whole genome sequences.
>
> Best regards
> Lee
>
> --
> Dr Lee Hazelwood
> BHRC Bioinformatics Technology Group Leader
> Biomedical and Health Research Centre
> Faculty of Biological Sciences
> Garstang Building,
> University of Leeds,
> Leeds,
> LS2 9JT, UK.
> E-mail: [hidden email]<mailto:[hidden email]>
>
>

Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org




_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Local Galaxy implimentation

Hans-Rudolf Hotz
Hi Lee

>>
>> *   What is a realistic amount of someones time to implement Galaxy on a Linux  server so that it can be used by researchers using the Web?

Galaxy is simple to set up and works out-of-the-box. You will have a
functional Galaxy server within minutes (yes, 'within minutes').


Providing Galaxy in a production environment will need a few extra steps
(see:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer 
). Depending on your needs, not all the steps are required. I highly
recommend, that you use PostgreSQL or MySQL (instead of the built in
SQLite) from day 1. Nevertheless, you should have a reliable server
within a few days.


>> *   What is the usual time overhead to keep it running and how skilled would they have to be?

Galaxy itself needs hardly any maintenance. However, it is advised to
update the code on a regularly basis. Currently we do it every three
months. We have a test and a production server, so the update process is
split over two days, with a couple of days testing in between. The
actual code updates have been very smooth so far and require about an
hour of downtime.

As long as you have support from your IT-Department running the
hardware, you don't need extraordinary skills. Galaxy is written in
Python, but you don't need to be a Python programmer (even if you want
to make a few changes), as long as you have some basic programming
skills in another language.

There is a lot of information on the wiki (sometimes, the info is
difficult to find). And if you get stuck, you can always send an e-mail
to "galaxy-dev"

Of course, it all changes when you add your own tools. Although, the
actual addition is simple. You might need some extra time for testing
and improving your tools. Also, don't forget the time required to teach
the use of Galaxy in general and the use of the self-written tools to
your colleagues at the bench.

Regards, Hans




Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland


>>
>> I should say, this will be for local biological researchers only, approx 20-30 dealing in Exome and Whole genome sequences.
>>
>> Best regards
>> Lee
>>
>> --
>> Dr Lee Hazelwood
>> BHRC Bioinformatics Technology Group Leader
>> Biomedical and Health Research Centre
>> Faculty of Biological Sciences
>> Garstang Building,
>> University of Leeds,
>> Leeds,
>> LS2 9JT, UK.
>> E-mail: [hidden email]<mailto:[hidden email]>
>>
>>
>
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
>
>
>
>
> _______________________________________________
> To manage your subscriptions to this and other Galaxy lists, please use the interface at:
>
>    http://lists.bx.psu.edu/
_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Local Galaxy implimentation

Nate Coraor (nate@bx.psu.edu)
In reply to this post by Anton Nekrutenko
Hi Lee,

If setting up Galaxy on an existing supported cluster, I would estimate
the setup time for an experienced sysadmin to be a day or two, although
that number can be larger if a lot of tools that depend on external
binaries (e.g. NGS mappers) and locally cached reference genomes are
desired, or you'd like to use the Sample Tracking/sequencer integration
features.

Once running, it usually only needs intervention if more disk space is
needed, or to perform updates to new versions.  New stable versions are
released about once a month and should usually only take about 10
minutes to apply, although we reccommend reading the accompanying
Development News Brief.  Reading the brief ensures there aren't any
surprises, and to be made aware of any new configuration options or
features.  This task is fairly simple but a basic to intermediate
knowledge of system administration will be helpful here.

You may want to have your staff review the documentation at
http://usegalaxy.org/production to get an idea of what's involved in
setting up a production Galaxy server.

Anton Nekrutenko wrote:

> Lee:
>
> I am CC'ing you e-mail to galaxy-dev list. You can get a lot of useful answers by posting to this list. Maintaining Galaxy is not different from maintaining other software resources. To run it locally you will need to have a system administration supervision as with any other high performance system. It is wonderful that you are sending your staff members to Galaxy Community Conference as they will be able to interact with key Galaxy Team members such as Nate Coraor, who runs Penn State instance here.
>
> Thanks!
>
> anton
>
>
>
> On Feb 25, 2011, at 6:14 AM, Lee Hazelwood wrote:
>
> > Dear Prof Nekrutenko,
> >
> > The university where I work is looking to locally implement your elegant software to enable us to view and analyse the rapidly growing amount of sequence data. We will be sending two staff members to the conference in Lunteren in May to get right into the detail on how we would achieve this.
> >
> > However, with all things I need to request some time/ support for running such a system in advance of May.
> > If you could help by briefly answering the questions below I would much appreciate it.
> >
> > *   What is a realistic amount of someones time to implement Galaxy on a Linux  server so that it can be used by researchers using the Web?
> > *   What is the usual time overhead to keep it running and how skilled would they have to be?
> >
> > I should say, this will be for local biological researchers only, approx 20-30 dealing in Exome and Whole genome sequences.
> >
> > Best regards
> > Lee
> >
> > --
> > Dr Lee Hazelwood
> > BHRC Bioinformatics Technology Group Leader
> > Biomedical and Health Research Centre
> > Faculty of Biological Sciences
> > Garstang Building,
> > University of Leeds,
> > Leeds,
> > LS2 9JT, UK.
> > E-mail: [hidden email]<mailto:[hidden email]>
> >
> >
>
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
>
>
>
>
> _______________________________________________
> To manage your subscriptions to this and other Galaxy lists, please use the interface at:
>
>   http://lists.bx.psu.edu/
_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/