Re: [Gmod-ajax] [Gmod-gbrowse] Creating a 'complete' GMOD virtual machine for distribution

[Ian H. <ih...@be...>]

Todd -- makes sense -- thanks for the info
Ian

Todd Harris wrote:
> Hi Scott, Ian -
> 
> Here's my take on Knoppix/liveCD having just rolled out a VMWare 
> virtualization project for WormBase.
> 
> With a goal for creating an easy system for archiving as a well as a way 
> for "bioinformatically naive" users to run WormBase locally I decided 
> against knoppix for a number of reasons, in order of importance.  I 
> reserve the right to be completely wrong on any of these points since 
> it's been almost a year since I touched knoppix.
> 
> 1.  Knoppix/liveCD approaches are limited to media size.
> 
> WormBase was too big for a DVD.  This might not be a limit for GMOD.
> 
> 2.  Networking.  I couldn't figure out how to bridge knoppix to the host.
> 
> 3. VMXs are easy and free to create and simple to use.
> 
> The release of VMServer last fall now means that a licensed commercial 
> copy of VMWare Workstation is not longer required to create VMXs.  They 
> run on Mac, Windows, and Linux very well with *almost* double-click 
> simplicity.
> 
> 4. Knoppix is most easily run from a CD, not the hard drive.  This 
> didn't allow for suitable performance of a WormBase application.
> 
> 5. Knoppix isn't open-virtualization.  It's a specific (Debian-based) 
> distro of Linux.  I wanted to run a different distribution.
> 
> Todd
> 
> 
> On Mar 22, 2007, at 9:36 PM, Scott Cain wrote:
> 
>> On Thu, 2007-03-22 at 12:29 -0700, Ian Holmes wrote:
>>> Scott, this sounds great.
>>>
>>> I would love to see our ongoing extensions to GBrowse (Ajax, wiki...) in
>>> something like this.
>>>
>>> Can I ask why use VMware instead of e.g. a liveCD or Knoppix type
>>> arrangement?
>>
>> Um, I dunno, VMware is the technology that Lincoln told me about--I've
>> done virtually no research other than to try it out and find that it
>> works.  The other day I was running a linux host while listen to iTunes
>> running inside of a Windows guest streaming from my wife's Mac.  The
>> ability to easily move between a host OS and the guest VM is pretty
>> appealing.
>>
>> I guess one thing I like about VMware is the ease of creation.  If I
>> create a VM that has chado and GBrowse installed in it, and someone else
>> wants to add Apollo, all they have to do is get my VM, add it and resave
>> it (at least in theory, that I haven't tried out).
>>
>> Scott
>>
>>>
>>> Ian
>>>
>>>
>>>
>>> Scott Cain wrote:
>>>> Hello,
>>>>
>>>> Recently, the people in my lab have been experimenting a lot with 
>>>> VMware
>>>> for creating virtual machines.  I am excited about the potential uses
>>>> for these virtual machines for several purposes, among them the ability
>>>> to create a consistent platform for teaching (like giving a classroom a
>>>> disk with the VMware player and a linux VM with GBrowse preinstalled to
>>>> give a tutorial), and for creating virtual machines that could be used
>>>> as a 'test server' that people interested in GMOD software could get 
>>>> and
>>>> try out without having to set up a server to do it.  That is what this
>>>> email is about.
>>>>
>>>> My goal is two-fold: first I am looking for volunteers.  If anybody
>>>> would like to under take the task of creating a virtual machine and
>>>> populate it with GMOD software and sample data, I would be thrilled to
>>>> give guidance and moral support.
>>>>
>>>> Second, I want to get feedback on what should be installed. There is
>>>> both the question of sample data and software.  Here are my thoughts so
>>>> far:
>>>>
>>>>   Chado and related core components
>>>>   XORT
>>>>   GBrowse
>>>>   Apollo
>>>>   CMap
>>>>   Turnkey/gmod-web
>>>>   BLAST graphic viewer
>>>>
>>>> Also, there are some things 'on the bubble' that I haven't decided
>>>> whether they should be installed:
>>>>
>>>>   Sybil
>>>>   Flash GViewer
>>>>   Textpresso
>>>>   BioMart
>>>>   DAS2 server
>>>>
>>>> Any thoughts on these?
>>>>
>>>> Thanks for your time,
>>>> Scott
>>>>
>>>>
>>>>
>>>>
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>>
>> Scott Cain, Ph. D.                                   cai...@gm...
>> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
>> Cold Spring Harbor Laboratory
>>
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