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[bioontology-support] Fwd: Re: ncbo appliance

Rhett Hillary rhett at profectushealthresearch.com
Wed Jul 25 09:52:32 PDT 2012


Hello,

I am after the status of the BioPortal VM image. Is there a newer 
version than 0.5? If so could you please provide a link?

Regards,

Rhett Hillary


-------- Original Message --------
Subject: 	Re: ncbo appliance
Date: 	Wed, 25 Jul 2012 09:49:29 -0700
From: 	Rhett Hillary <rhett at profectushealthresearch.com>
To: 	Trish Whetzel <whetzel at stanford.edu>
CC: 	Tony Martin <tony at profectushealthresearch.com>, marc <marc at cybre.net>



Hi Trish,

Has the new BioPortal VM appliance been released yet? If so could you 
please provide me with a link?

Regards,

Rhett Hillary

-------- Original Message --------
Subject: Re: ncbo appliance
From: Trish Whetzel <whetzel at stanford.edu>
To: Rhett Hillary <rhett at profectushealthresearch.com>
Date: 05/30/2012 04:59 PM
> Are you using the ovftool?
>
> Sent from my iPhone
>
> On May 30, 2012, at 3:38 PM, Rhett Hillary 
> <rhett at profectushealthresearch.com 
> <mailto:rhett at profectushealthresearch.com>> wrote:
>
>> Hi Trish,
>>
>> Yes I followed the instructions
>>
>> for disk in `ls -1 *.vmdk`; do diskbase=`basename $disk .vmdk`; 
>> qemu-img convert -O raw ${diskbase}.vmdk ${diskbase}.img; done
>>
>> *qemu-img: error while reading sector 131072: Invalid argument
>> qemu-img: error while reading sector 131072: Invalid argument
>> *
>> But it does create the disk images so I continued and created the XML 
>> file tried to start it. See below
>>
>> https://dl.dropbox.com/u/906920/screenshots/screenshot-20120530153650.jpeg
>>
>> Rhett
>>
>>
>> On 05/30/2012 03:16 PM, Trish Whetzel wrote:
>>> Are you following the instructions at:
>>> http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#KVM
>>>
>>> In addition, a new version of the VM is currently being generated. 
>>> New versions are generated quarterly.
>>>
>>> Trish
>>>
>>>
>>> On May 30, 2012, at 2:59 PM, Rhett Hillary wrote:
>>>
>>>> Hello,
>>>>
>>>> We (UCSF) are attempting to install the BioPortal VM under KVM. I 
>>>> have tried almost everything to convert the disk files but they 
>>>> fail. Is the
>>>> wgethttp://www.bioontology.org/ncbo-appliance/ncbo-appliance-0.5.zip
>>>> The correct link?? I have followed the wiki and are unable to 
>>>> convert the files. They dont even seem to work under vmware player 
>>>> in window.
>>>>
>>>> Kind Regards,
>>>>
>>>> Rhett Hillary
>>>>
>>>>
>>>> -------- Original Message --------
>>>> Subject: 	Re: ncbo
>>>> Date: 	Wed, 30 May 2012 14:55:22 -0700 (PDT)
>>>> From: 	marc <marc at cybre.net <mailto:marc at cybre.net>>
>>>> To: 	Rhett Hillary <rhett at rhett.cc <mailto:rhett at rhett.cc>>
>>>> CC: 	Tony Martin <tony at profectushealthresearch.com 
>>>> <mailto:tony at profectushealthresearch.com>>
>>>>
>>>>
>>>>
>>>> Perhaps you should ask:whetzel at stanford.edu  <mailto:whetzel at stanford.edu>  for some guidance?
>>>>
>>>> On Wed, 30 May 2012, Rhett Hillary wrote:
>>>>
>>>> > It seems this download is corrupted.. I tried converting the images to KVM on
>>>> > linux and no luck. I tried importing them into VirtualBox.. no luck. Then I
>>>> > tried importing the images to vmware player on windows, no luck. I think
>>>> > there is something wrong with the disk files.
>>>> >
>>>> > How can we mail about this?
>>>> >
>>>> > Rhett
>>>> >
>>>> > On 05/23/2012 01:23 PM, marc wrote:
>>>> >>
>>>> >> wgethttp://www.bioontology.org/ncbo-appliance/ncbo-appliance-0.5.zip
>>>> >>
>>>> >>
>>>> >>
>>>> >> On Wed, 23 May 2012, Rhett Hillary wrote:
>>>> >>
>>>> >>> If it needs more then we shouldnt be doing this in a VM.. I'll download it
>>>> >>> directly to the host..Just give me the link and I will tell you when it is
>>>> >>> done.
>>>> >>>
>>>> >>> Rhett
>>>> >>>
>>>> >>> On 05/23/2012 12:51 PM, marc wrote:
>>>> >>>> Hey Rhett,
>>>> >>>>
>>>> >>>> I've downloaded what appears to be a VM image for ncbo bioportal that I'd
>>>> >>>> like to take a look at.  Its sizable and I'd like for you to make the
>>>> >>>> /mnt/data partition mounted on dev-teiid writable so that I can plop it
>>>> >>>> down there, unzip it and have a look see.
>>>> >>>>
>>>> >>>> Is that possible?
>>>> >>>>
>>>> >>>> thanks,
>>>> >>>>
>>>> >>>> -marc
>>>> >>>>
>>>> >>>
>>>> >
>>>
>>>
>>




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