Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Fwd: Re: ncbo appliance

Trish Whetzel whetzel at stanford.edu
Wed Jul 25 10:18:04 PDT 2012


Hi Rhett, 

Can you send your BioPortal username?

Trish 



On Jul 25, 2012, at 6:52 PM, Rhett Hillary wrote:

> 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> 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 
>>>>> wget http://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>
>>>>> To:	Rhett Hillary <rhett at rhett.cc>
>>>>> CC:	Tony Martin <tony at profectushealthresearch.com>
>>>>> 
>>>>> Perhaps you should ask: 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:
>>>>> >> 
>>>>> >> wget http://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
>>>>> >>>> 
>>>>> >>> 
>>>>> >
>>>> 
>>>> 
>>> 
> 
> 
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20120725/460edf4d/attachment-0001.html>


More information about the bioontology-support mailing list